| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20160928_164738_883 |
| Start time | 2016-09-28 16:47:38 |
| Run time | 22:51:40.851 |
| Tasks executed | 16 |
| Tasks failed | 1 |
| Tasks failed names | spp rep1 |
| Arguments* | [-title, ZF5, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF5_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20160928_164738_883/task.callpeak_spp.spp_rep1.line_54.id_25 |
| thread_42 | thread_Root | chipseq.bds.20160928_164738_883_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_11 chipseq.bds.20160928_164738_883_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12 chipseq.bds.20160928_164738_883_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_13 chipseq.bds.20160928_164738_883_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_14 chipseq.bds.20160928_164738_883_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_15 chipseq.bds.20160928_164738_883_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_16 |
| thread_41 | thread_Root | chipseq.bds.20160928_164738_883_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_10 chipseq.bds.20160928_164738_883_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_17 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bam.dedup_bam_1_rep1.line_95.id_18 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bam.markdup_bam_picard_rep1.line_347.id_19 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bam.dedup_bam_2_rep1.line_144.id_20 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bam.bam_to_tag_rep1.line_504.id_21 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bed.subsample_tag_rep1.line_41.id_22 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bed.spr_rep1.line_247.id_23 chipseq.bds.20160928_164738_883_parallel_41/task.postalign_bed.xcor_rep1.line_205.id_24 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 113
bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF5_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 12277 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 181.93 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 180.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 179.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 174.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 176.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 184.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 190.01 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 193.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 191.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 198.56 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 203.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 193.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 189.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 189.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 190.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 188.43 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.61 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 188.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 192.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 189.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 191.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 191.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 188.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 188.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 190.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 191.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 177.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 173.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 172.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 172.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 172.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 175.09 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 172.07 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 176.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 180.17 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 174.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 167.93 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 161.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 164.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 179.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 191.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 190.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 188.71 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 186.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 183.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 177.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 180.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 185.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 188.30 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 177.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 176.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 176.71 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 171.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 174.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 174.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 174.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 178.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 175.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 170.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 170.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 175.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 177.94 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 179.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 184.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 177.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 182.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 114.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.33 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.01 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.55 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.62 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.71 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 28.05 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 212.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 210.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 205.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 215.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 193.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 210.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 181.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 193.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 205.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 211.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 246.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 248.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 212.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 185.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 192.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 194.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 200.94 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 210.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 214.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 207.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 202.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 192.79 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 192.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 194.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 190.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 201.16 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 206.39 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 205.50 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 209.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 210.24 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 207.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 186.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.11 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 187.06 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 182.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 178.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 155.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 154.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 152.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 152.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 153.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 152.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 153.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 174.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 157.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 156.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 155.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 153.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 153.95 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 147.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 141.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.42 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 127.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 127.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 127.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.05 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 154.84 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 155.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 156.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 158.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 148.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.30 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.05 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 21.19 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 50331648 sequences have been processed. [bwa_read_seq] 5.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 50593792 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 101.11 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 50855936 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 154.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 51118080 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 153.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 51380224 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 153.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 51642368 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 152.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 51904512 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 150.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 52166656 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 143.98 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 52428800 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.42 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 52690944 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 52953088 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 53215232 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 53477376 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.31 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 53739520 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 54001664 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.21 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 54263808 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 54525952 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 54788096 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.63 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 55050240 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.09 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 55312384 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 55574528 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.88 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 55836672 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.00 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 56098816 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.20 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 56360960 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.31 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 56623104 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 56885248 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.88 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 57147392 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 57409536 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 57671680 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 57933824 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 143.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 58195968 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 130.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 58458112 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 58720256 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 146.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 58982400 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 59244544 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 59506688 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 144.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 59768832 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 146.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 60030976 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 60293120 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 60555264 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.00 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 60817408 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 61079552 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.37 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 61341696 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.18 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 61603840 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 61865984 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 62128128 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 62390272 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 62652416 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 62914560 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 63176704 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 63438848 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 130.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 63700992 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 63963136 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 64225280 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.09 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 64487424 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 64749568 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.49 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 65011712 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 65273856 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 65536000 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 65798144 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66060288 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66322432 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 130.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 66584576 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66846720 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.07 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 67108864 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.66 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 67371008 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 67633152 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.94 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 67895296 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 68157440 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 68419584 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 68681728 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 68943872 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 69206016 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 69468160 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 69730304 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 69992448 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 70254592 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 70516736 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 70778880 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 71041024 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 71303168 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 71565312 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 71827456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 72089600 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 72351744 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 72613888 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 20.46 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 72876032 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 73138176 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 73400320 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 73662464 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.50 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 73924608 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 74186752 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 74448896 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 74711040 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 74973184 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 19.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 75235328 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.61 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 75497472 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 156.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 75759616 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 156.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 76021760 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 157.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 76283904 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 157.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 76546048 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 156.39 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 76808192 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 77070336 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 77332480 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 143.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 77594624 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 77856768 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78118912 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78381056 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.64 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 78643200 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 141.35 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 78905344 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 79167488 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.33 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 79429632 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.49 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 79691776 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.94 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 79953920 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 80216064 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.50 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 80478208 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 80740352 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 81002496 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 81264640 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 145.20 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 81526784 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 141.04 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 81788928 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 82051072 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 82313216 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 82575360 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 141.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 82837504 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 143.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 83099648 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 147.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 83361792 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.49 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 83623936 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 83886080 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 84148224 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 130.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 84410368 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 84672512 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 84934656 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 85196800 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 85458944 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 85721088 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 85983232 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.03 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 86245376 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 86507520 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 86769664 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 87031808 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 87293952 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 87556096 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 87818240 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 88080384 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.94 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 88342528 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 143.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 88604672 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 88866816 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.59 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 89128960 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 89391104 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 140.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 89653248 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 89915392 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.84 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 90177536 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.88 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 90439680 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 90701824 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 90963968 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 91226112 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.62 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 91488256 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 91750400 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.79 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 92012544 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 92274688 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 92536832 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 92798976 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 123.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 93061120 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 123.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 93323264 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 93585408 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 123.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 93847552 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 122.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 94109696 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 121.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 94371840 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 108.60 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 94633984 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.93 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 94896128 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.93 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 95158272 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 95420416 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 95682560 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 95944704 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 96206848 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 96468992 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 96731136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 96993280 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 97255424 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 97517568 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 97779712 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.05 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 98041856 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 98304000 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.46 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 98566144 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 98828288 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.94 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 99090432 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 99352576 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 99614720 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 99876864 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.84 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 100139008 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 8.78 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 100401152 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 4.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 100663296 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 100925440 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101187584 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101449728 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101711872 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101974016 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 102236160 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 102498304 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 102760448 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 103022592 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.13 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 103284736 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.01 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 103546880 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 103809024 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 104071168 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.14 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 104333312 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 104595456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 104857600 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.33 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 105119744 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.31 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 105381888 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.08 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 105644032 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.05 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 105906176 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 106168320 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 106430464 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.16 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 106692608 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 106954752 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 107216896 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 107479040 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 107741184 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 108003328 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 108265472 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 108527616 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 108789760 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.16 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 109051904 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 109314048 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 109576192 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.27 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 109838336 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 110100480 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.32 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 110362624 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 110624768 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 110886912 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 111149056 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 111411200 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 111673344 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 111935488 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.37 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 112197632 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 112459776 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.27 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 112721920 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 112984064 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 113246208 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 113508352 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.15 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 113770496 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 114032640 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 114294784 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.06 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 114556928 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 114819072 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 115081216 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 115343360 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 115605504 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 115867648 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.10 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 116129792 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 116391936 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 116654080 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 116916224 sequences have been processed. [bwa_read_seq] 4.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 117178368 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 117440512 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 117702656 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.13 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 117964800 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 118226944 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.34 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 118489088 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 118751232 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 119013376 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 119275520 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 3.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 119537664 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 2.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 119799808 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.82 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 120061952 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.78 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 120324096 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.73 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 120586240 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 120848384 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.82 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 121110528 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.82 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 121372672 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.76 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 121634816 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.90 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 121896960 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.77 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 122159104 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.79 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 122421248 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.72 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 122683392 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 122945536 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 123207680 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.69 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 123469824 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.73 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 123731968 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 123994112 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 124256256 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.63 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 124518400 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.81 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 124780544 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 1.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 125042688 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 125304832 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 156.32 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 125566976 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 125829120 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 126091264 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 126353408 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 139.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 126615552 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 126877696 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 127139840 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.14 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 127401984 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 112.75 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 127664128 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 117.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 127926272 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 142.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 128188416 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.54 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 128450560 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 108.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 128712704 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 120.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 128974848 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.30 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 129236992 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 129499136 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 129761280 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 137.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 130023424 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 138.77 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 130285568 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 136.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 130547712 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.83 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 130809856 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 131072000 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 135.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 131334144 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 133.79 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 131596288 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 131858432 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.09 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 132120576 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 132382720 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 132644864 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 132907008 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 133169152 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 133431296 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 123.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 133693440 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 104.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 133955584 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 102.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 134217728 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 115.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 134479872 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 134742016 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.71 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 135004160 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 122.79 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 135266304 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 135528448 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 123.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 135790592 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 136052736 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 123.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 136314880 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 122.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 136577024 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 136839168 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 125.75 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 137101312 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 127.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 137363456 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 128.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 137625600 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 134.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 137887744 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 138149888 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 132.64 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 138412032 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 130.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 138674176 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 138936320 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 126.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 139198464 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 139460608 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 131.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 139722752 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 105.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 139984896 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 140247040 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 120.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 140509184 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 129.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 140771328 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 124.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 141033472 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 121.31 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 141295616 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 119.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 141557760 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 119.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 141819904 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 142082048 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 142344192 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 142606336 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 142868480 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 117.31 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 143130624 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 117.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 143392768 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 143654912 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 116.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 143917056 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 118.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 144179200 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 111.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 144441344 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 144703488 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 144965632 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 145227776 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 145489920 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 145752064 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 146014208 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 146276352 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 146538496 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.00 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 146800640 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 147062784 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 147324928 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.83 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 147587072 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 147849216 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 18.16 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 148111360 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 148373504 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 148635648 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 148897792 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149159936 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149422080 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149684224 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 17.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149946368 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 150208512 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 150470656 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 150732800 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 150994944 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 151257088 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.94 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 151519232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 151781376 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 152043520 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 152305664 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.46 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 152567808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 152829952 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 153092096 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 153354240 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 153616384 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 153878528 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 154140672 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 154402816 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 154664960 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 154927104 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 155189248 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.98 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 155451392 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 155713536 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 155975680 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 156237824 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 156499968 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 156762112 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 157024256 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 157286400 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 157548544 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 157810688 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 158072832 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 158334976 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 158597120 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 158859264 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 159121408 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 159383552 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.07 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 159645696 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.64 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 159907840 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 160169984 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 160432128 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 160694272 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 160956416 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.25 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 161218560 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 161480704 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 161742848 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.39 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 162004992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.74 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 162267136 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 162529280 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 162791424 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 163053568 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.98 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 163315712 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 163577856 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 163840000 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 164102144 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 164364288 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 164626432 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 164888576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.90 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 165150720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 165412864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 165675008 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 165937152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 166199296 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.93 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 166461440 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 166723584 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 166985728 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 167247872 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 167510016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 167772160 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.88 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 168034304 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.50 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 168296448 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 168558592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 168820736 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 169082880 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 169345024 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 169607168 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 169869312 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 170131456 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.64 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 170393600 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 170655744 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 170917888 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 171180032 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 171442176 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 171704320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 171966464 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 172228608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 172490752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 172752896 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 173015040 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 173277184 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 173539328 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 173801472 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 174063616 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 174325760 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 174587904 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 174850048 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 175112192 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 175374336 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 175636480 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 175898624 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 176160768 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 176422912 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 176685056 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 176947200 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 177209344 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 177471488 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.07 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 177733632 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 177995776 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 178257920 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.89 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 178520064 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 178782208 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 179044352 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 179306496 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 179568640 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 179830784 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 180092928 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 180355072 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 180617216 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 180879360 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 181141504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.26 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 181403648 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 181665792 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.23 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 181927936 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 182190080 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 182452224 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 182714368 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 182976512 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 183238656 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 183500800 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 183762944 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184025088 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184287232 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.21 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184549376 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184811520 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 185073664 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 185335808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 185597952 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 185860096 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 186122240 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 186384384 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 186646528 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 186908672 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.31 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 187170816 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 187432960 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 187695104 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 187957248 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 188219392 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 188481536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 188743680 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 189005824 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 189267968 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 189530112 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 189792256 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 190054400 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 190316544 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 190578688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 190840832 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 191102976 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.69 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 191365120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 191627264 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 191889408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 192151552 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 192413696 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 192675840 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 192937984 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 193200128 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 193462272 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.26 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 193724416 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.19 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 193986560 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 194248704 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.54 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 194510848 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.32 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 194772992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.21 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 195035136 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 195297280 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 195559424 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 195821568 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 196083712 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 196345856 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 196608000 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 196870144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.90 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 197132288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.60 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 197394432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 197656576 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 197918720 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 198180864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.74 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 198443008 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 198705152 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 198967296 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 199229440 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 199491584 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 199753728 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 200015872 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 200278016 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.89 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 200540160 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.62 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 200802304 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 201064448 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 201326592 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 201588736 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 201850880 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 202113024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.19 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 202375168 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 202637312 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 202899456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 203161600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 203423744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 203685888 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 203948032 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 204210176 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 204472320 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 204734464 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 204996608 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 205258752 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 205520896 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 205783040 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 206045184 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 206307328 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 206569472 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 206831616 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.08 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 207093760 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.74 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 207355904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 207618048 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 207880192 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 208142336 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 208404480 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 208666624 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 208928768 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 209190912 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 209453056 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 209715200 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 209977344 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 210239488 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 210501632 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 210763776 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 211025920 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.08 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 211288064 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 211550208 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 211812352 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 212074496 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 212336640 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 212598784 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 212860928 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 213123072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 213385216 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 213647360 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 213909504 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 214171648 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 214433792 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 214695936 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 214958080 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 215220224 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 215482368 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.93 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 215744512 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 216006656 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 216268800 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 216530944 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 216793088 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 217055232 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 217317376 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 217579520 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 217841664 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218103808 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218365952 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218628096 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218890240 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 219152384 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.19 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 219414528 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 219676672 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 219938816 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 220200960 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 220463104 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 220725248 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 220987392 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 221249536 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 221511680 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.88 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 221773824 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 222035968 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 222298112 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 222560256 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 222822400 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 223084544 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 223346688 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 223608832 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.89 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 223870976 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 224133120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.93 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 224395264 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 224657408 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 224919552 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 225181696 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 225443840 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 225705984 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 70.70 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 225968128 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 226230272 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 226492416 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 226754560 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 13.61 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 226802161 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa aln -q 5 -l 32 -k 2 -t 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF5_allReps.fastq.gz [main] Real time: 19681.641 sec; CPU: 75657.912 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 110
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 113
bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.sai
# SYS command. line 115
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 4831 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 26.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.73 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.51 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.53 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.38 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.43 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.41 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.75 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.66 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.70 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.56 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.94 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.77 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.91 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.17 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.17 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.87 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.56 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 27.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 7.77 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 23141323 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa aln -q 5 -l 32 -k 2 -t 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz [main] Real time: 2804.398 sec; CPU: 2805.860 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/ctl1/mousePrimaryBCellInput.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 3935 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.73 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.50 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.44 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.27 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.80 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.28 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.92 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.65 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.66 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.60 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.74 sec [bwa_aln_core] refine gapped alignments... 0.69 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.71 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.36 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.23 sec [bwa_aln_core] refine gapped alignments... 0.58 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.77 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.26 sec [bwa_aln_core] refine gapped alignments... 0.56 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.11 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.88 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.77 sec [bwa_aln_core] refine gapped alignments... 0.52 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.20 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.62 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.91 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.65 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.42 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.03 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.62 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.38 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.35 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.37 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.84 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.67 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.37 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.23 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.41 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.93 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.89 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.80 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.80 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.85 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.86 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.94 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.02 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.99 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.76 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.32 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.45 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.27 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.07 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.12 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.22 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.28 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.42 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.54 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.96 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.93 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.49 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.89 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.13 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.94 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.68 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.17 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.51 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.09 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.03 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.08 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.95 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.96 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.78 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.91 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.96 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.87 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.27 sec [bwa_aln_core] refine gapped alignments... 0.28 sec [bwa_aln_core] print alignments... 0.14 sec [bwa_aln_core] 23141323 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz [main] Real time: 484.903 sec; CPU: 408.136 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 11702 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 349
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 353
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 354
export MAX_JAVA_MEM="12G"
# SYS command. line 359
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 368
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/ctl1/mousePrimaryBCellInput.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/ctl1/mousePrimaryBCellInput.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 4234 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Wed Sep 28 17:57:22 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/ctl1/mousePrimaryBCellInput.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Sep 28 17:57:22 PDT 2016] Executing as imk1@kali on Linux 3.19.0-64-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory) INFO 2016-09-28 17:57:22 MarkDuplicates Start of doWork freeMemory: 255390032; totalMemory: 257294336; maxMemory: 3817799680 INFO 2016-09-28 17:57:22 MarkDuplicates Reading input file and constructing read end information. INFO 2016-09-28 17:57:22 MarkDuplicates Will retain up to 15149998 data points before spilling to disk. INFO 2016-09-28 17:57:27 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:174,151,470 INFO 2016-09-28 17:57:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:31 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr2:135,780,411 INFO 2016-09-28 17:57:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:34 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr3:122,530,375 INFO 2016-09-28 17:57:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:37 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr4:135,044,888 INFO 2016-09-28 17:57:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:40 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr5:135,067,778 INFO 2016-09-28 17:57:40 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:44 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr6:144,681,933 INFO 2016-09-28 17:57:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:47 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr8:12,749,386 INFO 2016-09-28 17:57:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:53 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 5s. Last read position: chr9:42,425,131 INFO 2016-09-28 17:57:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:57:58 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 5s. Last read position: chr10:69,658,983 INFO 2016-09-28 17:57:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:02 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr11:86,536,377 INFO 2016-09-28 17:58:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:06 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 4s. Last read position: chr13:6,026,344 INFO 2016-09-28 17:58:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:10 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: chr14:54,434,282 INFO 2016-09-28 17:58:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:15 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 5s. Last read position: chr15:98,839,731 INFO 2016-09-28 17:58:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:18 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr17:62,456,013 INFO 2016-09-28 17:58:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:21 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr19:38,585,732 INFO 2016-09-28 17:58:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-28 17:58:30 MarkDuplicates Read 15489502 records. 0 pairs never matched. INFO 2016-09-28 17:58:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 2052750088; totalMemory: 2129395712; maxMemory: 3817799680 INFO 2016-09-28 17:58:30 MarkDuplicates Will retain up to 119306240 duplicate indices before spilling to disk. INFO 2016-09-28 17:58:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-09-28 17:58:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-09-28 17:58:39 MarkDuplicates Sorting list of duplicate records. INFO 2016-09-28 17:58:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 1400148984; totalMemory: 2370371584; maxMemory: 3817799680 INFO 2016-09-28 17:58:40 MarkDuplicates Marking 157890 records as duplicates. INFO 2016-09-28 17:58:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-09-28 18:00:30 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:50s. Time for last 10,000,000: 110s. Last read position: chr11:86,536,377 INFO 2016-09-28 18:01:30 MarkDuplicates Before output close freeMemory: 2087092688; totalMemory: 2104688640; maxMemory: 3817799680 INFO 2016-09-28 18:01:31 MarkDuplicates After output close freeMemory: 2135326344; totalMemory: 2152923136; maxMemory: 3817799680 [Wed Sep 28 18:01:31 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 4.15 minutes. Runtime.totalMemory()=2152923136 | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/ctl1/mousePrimaryBCellInput.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/ctl1/mousePrimaryBCellInput.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 13207 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 506
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 509
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 5412 (process ID) old priority 0, new priority 10 Waiting for 27 seconds. --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF5_allReps.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.bam
# SYS command. line 149
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 46831 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 81.50 sec [bwa_aln_core] refine gapped alignments... 12.52 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.35 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 86.04 sec [bwa_aln_core] refine gapped alignments... 1.61 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.82 sec [bwa_aln_core] refine gapped alignments... 8.65 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 81.34 sec [bwa_aln_core] refine gapped alignments... 1.43 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 38.88 sec [bwa_aln_core] refine gapped alignments... 11.31 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.08 sec [bwa_aln_core] refine gapped alignments... 14.22 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.32 sec [bwa_aln_core] refine gapped alignments... 12.11 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.89 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 53.44 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.30 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.32 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.92 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.28 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.91 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 69.46 sec [bwa_aln_core] refine gapped alignments... 1.64 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 53.17 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.71 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.82 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.28 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.13 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.76 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.09 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 52.63 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.49 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.89 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.97 sec [bwa_aln_core] refine gapped alignments... 1.31 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.92 sec [bwa_aln_core] refine gapped alignments... 7.97 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 83.46 sec [bwa_aln_core] refine gapped alignments... 11.16 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.19 sec [bwa_aln_core] refine gapped alignments... 11.67 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 92.06 sec [bwa_aln_core] refine gapped alignments... 12.25 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.32 sec [bwa_aln_core] refine gapped alignments... 13.51 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 87.84 sec [bwa_aln_core] refine gapped alignments... 14.50 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 89.92 sec [bwa_aln_core] refine gapped alignments... 12.70 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 94.58 sec [bwa_aln_core] refine gapped alignments... 12.92 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 89.46 sec [bwa_aln_core] refine gapped alignments... 13.77 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.37 sec [bwa_aln_core] refine gapped alignments... 1.52 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.56 sec [bwa_aln_core] refine gapped alignments... 13.12 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.13 sec [bwa_aln_core] refine gapped alignments... 9.68 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.79 sec [bwa_aln_core] refine gapped alignments... 2.89 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.57 sec [bwa_aln_core] refine gapped alignments... 4.60 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.16 sec [bwa_aln_core] refine gapped alignments... 13.27 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.17 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.42 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.61 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.49 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.39 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.38 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.99 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.54 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.48 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.04 sec [bwa_aln_core] refine gapped alignments... 12.95 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 81.62 sec [bwa_aln_core] refine gapped alignments... 13.69 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 84.44 sec [bwa_aln_core] refine gapped alignments... 15.14 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.47 sec [bwa_aln_core] refine gapped alignments... 7.78 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.93 sec [bwa_aln_core] refine gapped alignments... 8.31 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.31 sec [bwa_aln_core] refine gapped alignments... 7.92 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.43 sec [bwa_aln_core] refine gapped alignments... 13.44 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.96 sec [bwa_aln_core] refine gapped alignments... 6.79 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.79 sec [bwa_aln_core] refine gapped alignments... 5.13 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.69 sec [bwa_aln_core] refine gapped alignments... 6.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.71 sec [bwa_aln_core] refine gapped alignments... 6.51 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 44.83 sec [bwa_aln_core] refine gapped alignments... 7.39 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.64 sec [bwa_aln_core] refine gapped alignments... 5.78 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.75 sec [bwa_aln_core] refine gapped alignments... 6.45 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.04 sec [bwa_aln_core] refine gapped alignments... 6.26 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.89 sec [bwa_aln_core] refine gapped alignments... 8.62 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.27 sec [bwa_aln_core] refine gapped alignments... 12.85 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.50 sec [bwa_aln_core] refine gapped alignments... 7.53 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.26 sec [bwa_aln_core] refine gapped alignments... 9.71 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.13 sec [bwa_aln_core] refine gapped alignments... 9.32 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.34 sec [bwa_aln_core] refine gapped alignments... 16.62 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 89.87 sec [bwa_aln_core] refine gapped alignments... 17.55 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.46 sec [bwa_aln_core] refine gapped alignments... 15.67 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 87.00 sec [bwa_aln_core] refine gapped alignments... 14.74 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 89.12 sec [bwa_aln_core] refine gapped alignments... 17.84 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 107.27 sec [bwa_aln_core] refine gapped alignments... 18.36 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 96.05 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 69.79 sec [bwa_aln_core] refine gapped alignments... 0.54 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.60 sec [bwa_aln_core] refine gapped alignments... 3.11 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.01 sec [bwa_aln_core] refine gapped alignments... 2.33 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.20 sec [bwa_aln_core] refine gapped alignments... 4.12 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 77.57 sec [bwa_aln_core] refine gapped alignments... 5.72 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.45 sec [bwa_aln_core] refine gapped alignments... 5.27 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.06 sec [bwa_aln_core] refine gapped alignments... 4.42 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 79.75 sec [bwa_aln_core] refine gapped alignments... 4.83 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.84 sec [bwa_aln_core] refine gapped alignments... 4.22 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.03 sec [bwa_aln_core] refine gapped alignments... 2.97 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.90 sec [bwa_aln_core] refine gapped alignments... 3.87 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.14 sec [bwa_aln_core] refine gapped alignments... 5.03 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.26 sec [bwa_aln_core] refine gapped alignments... 5.17 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.93 sec [bwa_aln_core] refine gapped alignments... 6.82 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 87.48 sec [bwa_aln_core] refine gapped alignments... 7.66 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 78.83 sec [bwa_aln_core] refine gapped alignments... 7.28 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.45 sec [bwa_aln_core] refine gapped alignments... 5.50 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 82.30 sec [bwa_aln_core] refine gapped alignments... 6.50 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 78.04 sec [bwa_aln_core] refine gapped alignments... 2.55 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.67 sec [bwa_aln_core] refine gapped alignments... 3.19 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.24 sec [bwa_aln_core] refine gapped alignments... 8.35 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.01 sec [bwa_aln_core] refine gapped alignments... 8.20 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 78.00 sec [bwa_aln_core] refine gapped alignments... 8.47 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 78.53 sec [bwa_aln_core] refine gapped alignments... 9.14 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.46 sec [bwa_aln_core] refine gapped alignments... 8.18 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 83.21 sec [bwa_aln_core] refine gapped alignments... 11.19 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 97.84 sec [bwa_aln_core] refine gapped alignments... 11.09 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 91.77 sec [bwa_aln_core] refine gapped alignments... 8.54 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.48 sec [bwa_aln_core] refine gapped alignments... 3.06 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.12 sec [bwa_aln_core] refine gapped alignments... 2.31 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.10 sec [bwa_aln_core] refine gapped alignments... 4.30 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.47 sec [bwa_aln_core] refine gapped alignments... 5.75 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.31 sec [bwa_aln_core] refine gapped alignments... 6.23 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.21 sec [bwa_aln_core] refine gapped alignments... 5.56 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.34 sec [bwa_aln_core] refine gapped alignments... 6.93 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 79.20 sec [bwa_aln_core] refine gapped alignments... 7.74 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.65 sec [bwa_aln_core] refine gapped alignments... 1.83 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.75 sec [bwa_aln_core] refine gapped alignments... 2.30 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.96 sec [bwa_aln_core] refine gapped alignments... 6.05 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.21 sec [bwa_aln_core] refine gapped alignments... 7.02 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.38 sec [bwa_aln_core] refine gapped alignments... 6.44 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.96 sec [bwa_aln_core] refine gapped alignments... 7.95 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.15 sec [bwa_aln_core] refine gapped alignments... 2.43 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.94 sec [bwa_aln_core] refine gapped alignments... 2.69 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.30 sec [bwa_aln_core] refine gapped alignments... 4.23 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.81 sec [bwa_aln_core] refine gapped alignments... 4.49 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 86.88 sec [bwa_aln_core] refine gapped alignments... 4.42 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.03 sec [bwa_aln_core] refine gapped alignments... 3.62 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.71 sec [bwa_aln_core] refine gapped alignments... 4.26 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.79 sec [bwa_aln_core] refine gapped alignments... 3.55 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.72 sec [bwa_aln_core] refine gapped alignments... 4.18 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.57 sec [bwa_aln_core] refine gapped alignments... 4.82 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.91 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.81 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.62 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.50 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.65 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.86 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.55 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 36.06 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 44.12 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 79.44 sec [bwa_aln_core] refine gapped alignments... 7.21 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 82.25 sec [bwa_aln_core] refine gapped alignments... 10.75 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 91.09 sec [bwa_aln_core] refine gapped alignments... 13.67 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.89 sec [bwa_aln_core] refine gapped alignments... 14.68 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 99.14 sec [bwa_aln_core] refine gapped alignments... 15.72 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 100.13 sec [bwa_aln_core] refine gapped alignments... 14.68 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.28 sec [bwa_aln_core] refine gapped alignments... 8.33 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.85 sec [bwa_aln_core] refine gapped alignments... 12.58 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.45 sec [bwa_aln_core] refine gapped alignments... 13.33 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.95 sec [bwa_aln_core] refine gapped alignments... 13.07 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.08 sec [bwa_aln_core] refine gapped alignments... 9.03 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.87 sec [bwa_aln_core] refine gapped alignments... 2.66 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.28 sec [bwa_aln_core] refine gapped alignments... 3.56 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.90 sec [bwa_aln_core] refine gapped alignments... 4.40 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.41 sec [bwa_aln_core] refine gapped alignments... 6.06 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.90 sec [bwa_aln_core] refine gapped alignments... 4.33 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.82 sec [bwa_aln_core] refine gapped alignments... 5.75 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.01 sec [bwa_aln_core] refine gapped alignments... 3.11 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.98 sec [bwa_aln_core] refine gapped alignments... 2.47 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.67 sec [bwa_aln_core] refine gapped alignments... 1.44 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.49 sec [bwa_aln_core] refine gapped alignments... 1.33 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.75 sec [bwa_aln_core] refine gapped alignments... 1.85 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.49 sec [bwa_aln_core] refine gapped alignments... 1.61 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.10 sec [bwa_aln_core] refine gapped alignments... 1.90 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.31 sec [bwa_aln_core] refine gapped alignments... 2.07 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.45 sec [bwa_aln_core] refine gapped alignments... 1.52 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.01 sec [bwa_aln_core] refine gapped alignments... 1.50 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 27.67 sec [bwa_aln_core] refine gapped alignments... 1.23 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.43 sec [bwa_aln_core] refine gapped alignments... 1.75 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 35.47 sec [bwa_aln_core] refine gapped alignments... 1.71 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.94 sec [bwa_aln_core] refine gapped alignments... 2.16 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.60 sec [bwa_aln_core] refine gapped alignments... 2.35 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.65 sec [bwa_aln_core] refine gapped alignments... 4.43 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.53 sec [bwa_aln_core] refine gapped alignments... 3.67 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.65 sec [bwa_aln_core] refine gapped alignments... 5.35 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.65 sec [bwa_aln_core] refine gapped alignments... 4.67 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.74 sec [bwa_aln_core] refine gapped alignments... 5.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.00 sec [bwa_aln_core] refine gapped alignments... 5.50 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.80 sec [bwa_aln_core] refine gapped alignments... 5.48 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.54 sec [bwa_aln_core] refine gapped alignments... 5.83 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.16 sec [bwa_aln_core] refine gapped alignments... 6.19 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.66 sec [bwa_aln_core] refine gapped alignments... 7.43 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.56 sec [bwa_aln_core] refine gapped alignments... 7.46 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.99 sec [bwa_aln_core] refine gapped alignments... 8.39 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.66 sec [bwa_aln_core] refine gapped alignments... 6.62 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.22 sec [bwa_aln_core] refine gapped alignments... 7.59 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.14 sec [bwa_aln_core] refine gapped alignments... 7.25 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.07 sec [bwa_aln_core] refine gapped alignments... 7.29 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.00 sec [bwa_aln_core] refine gapped alignments... 6.10 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.20 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 44.69 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 44.68 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 50331648 sequences have been processed. [bwa_read_seq] 5.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.24 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 50593792 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.21 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 50855936 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.61 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 51118080 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.25 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 51380224 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.17 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 51642368 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.99 sec [bwa_aln_core] refine gapped alignments... 0.50 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 51904512 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.88 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 52166656 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 50.54 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 52428800 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.03 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 52690944 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.96 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 52953088 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.35 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 53215232 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.75 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 53477376 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.85 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 53739520 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.76 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 54001664 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.06 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 54263808 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.32 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 54525952 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.58 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 54788096 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.43 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 55050240 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.95 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 55312384 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.58 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 55574528 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.80 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 55836672 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.19 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 56098816 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.64 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 56360960 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.06 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 56623104 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.68 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 56885248 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.11 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 57147392 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.80 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 57409536 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.82 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 57671680 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.08 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 57933824 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.98 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 58195968 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.48 sec [bwa_aln_core] refine gapped alignments... 0.80 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 58458112 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.79 sec [bwa_aln_core] refine gapped alignments... 6.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 58720256 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.38 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 58982400 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.75 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 59244544 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.79 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 59506688 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.22 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 59768832 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.80 sec [bwa_aln_core] refine gapped alignments... 4.19 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 60030976 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.84 sec [bwa_aln_core] refine gapped alignments... 11.07 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 60293120 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.76 sec [bwa_aln_core] refine gapped alignments... 13.94 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 60555264 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 73.22 sec [bwa_aln_core] refine gapped alignments... 12.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 60817408 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.51 sec [bwa_aln_core] refine gapped alignments... 4.32 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 61079552 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.89 sec [bwa_aln_core] refine gapped alignments... 6.94 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 61341696 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.53 sec [bwa_aln_core] refine gapped alignments... 11.14 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 61603840 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.29 sec [bwa_aln_core] refine gapped alignments... 12.17 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 61865984 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 79.31 sec [bwa_aln_core] refine gapped alignments... 13.16 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 62128128 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.51 sec [bwa_aln_core] refine gapped alignments... 11.30 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 62390272 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.72 sec [bwa_aln_core] refine gapped alignments... 5.15 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 62652416 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.32 sec [bwa_aln_core] refine gapped alignments... 7.67 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 62914560 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.62 sec [bwa_aln_core] refine gapped alignments... 6.28 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 63176704 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.67 sec [bwa_aln_core] refine gapped alignments... 3.07 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 63438848 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.55 sec [bwa_aln_core] refine gapped alignments... 9.78 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 63700992 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.73 sec [bwa_aln_core] refine gapped alignments... 3.83 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 63963136 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.13 sec [bwa_aln_core] refine gapped alignments... 11.62 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 64225280 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 81.57 sec [bwa_aln_core] refine gapped alignments... 10.22 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 64487424 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.40 sec [bwa_aln_core] refine gapped alignments... 11.52 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 64749568 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.99 sec [bwa_aln_core] refine gapped alignments... 10.54 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 65011712 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.12 sec [bwa_aln_core] refine gapped alignments... 0.48 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 65273856 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.50 sec [bwa_aln_core] refine gapped alignments... 6.09 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 65536000 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.72 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 65798144 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.95 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 66060288 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 53.51 sec [bwa_aln_core] refine gapped alignments... 2.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 66322432 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.39 sec [bwa_aln_core] refine gapped alignments... 3.05 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 66584576 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.05 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 66846720 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.44 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 67108864 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.54 sec [bwa_aln_core] refine gapped alignments... 0.90 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 67371008 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.83 sec [bwa_aln_core] refine gapped alignments... 0.88 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 67633152 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.99 sec [bwa_aln_core] refine gapped alignments... 0.59 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 67895296 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.18 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 68157440 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.71 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 68419584 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.14 sec [bwa_aln_core] refine gapped alignments... 1.57 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 68681728 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 33.22 sec [bwa_aln_core] refine gapped alignments... 3.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 68943872 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.94 sec [bwa_aln_core] refine gapped alignments... 4.24 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 69206016 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.83 sec [bwa_aln_core] refine gapped alignments... 4.63 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 69468160 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.44 sec [bwa_aln_core] refine gapped alignments... 4.42 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 69730304 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.43 sec [bwa_aln_core] refine gapped alignments... 4.62 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 69992448 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.73 sec [bwa_aln_core] refine gapped alignments... 4.68 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 70254592 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.31 sec [bwa_aln_core] refine gapped alignments... 4.24 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 70516736 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.74 sec [bwa_aln_core] refine gapped alignments... 5.07 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 70778880 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.08 sec [bwa_aln_core] refine gapped alignments... 5.20 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 71041024 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.56 sec [bwa_aln_core] refine gapped alignments... 4.81 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 71303168 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.85 sec [bwa_aln_core] refine gapped alignments... 4.92 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 71565312 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.37 sec [bwa_aln_core] refine gapped alignments... 5.11 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 71827456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 48.25 sec [bwa_aln_core] refine gapped alignments... 7.22 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 72089600 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.98 sec [bwa_aln_core] refine gapped alignments... 6.75 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 72351744 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 69.34 sec [bwa_aln_core] refine gapped alignments... 2.57 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 72613888 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.98 sec [bwa_aln_core] refine gapped alignments... 5.11 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 72876032 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.93 sec [bwa_aln_core] refine gapped alignments... 4.03 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 73138176 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.23 sec [bwa_aln_core] refine gapped alignments... 4.07 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 73400320 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.50 sec [bwa_aln_core] refine gapped alignments... 4.25 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 73662464 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 86.47 sec [bwa_aln_core] refine gapped alignments... 3.91 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 73924608 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.50 sec [bwa_aln_core] refine gapped alignments... 11.81 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 74186752 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.93 sec [bwa_aln_core] refine gapped alignments... 6.55 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 74448896 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.94 sec [bwa_aln_core] refine gapped alignments... 10.25 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 74711040 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.57 sec [bwa_aln_core] refine gapped alignments... 7.70 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 74973184 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.90 sec [bwa_aln_core] refine gapped alignments... 6.07 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 75235328 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.34 sec [bwa_aln_core] refine gapped alignments... 7.43 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 75497472 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.18 sec [bwa_aln_core] refine gapped alignments... 10.71 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 75759616 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.29 sec [bwa_aln_core] refine gapped alignments... 7.26 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 76021760 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.04 sec [bwa_aln_core] refine gapped alignments... 7.00 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 76283904 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.63 sec [bwa_aln_core] refine gapped alignments... 4.29 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 76546048 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.85 sec [bwa_aln_core] refine gapped alignments... 8.04 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 76808192 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.49 sec [bwa_aln_core] refine gapped alignments... 11.78 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 77070336 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 31.72 sec [bwa_aln_core] refine gapped alignments... 4.88 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 77332480 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.84 sec [bwa_aln_core] refine gapped alignments... 10.11 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 77594624 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.78 sec [bwa_aln_core] refine gapped alignments... 10.75 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 77856768 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.32 sec [bwa_aln_core] refine gapped alignments... 13.37 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 78118912 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.55 sec [bwa_aln_core] refine gapped alignments... 11.37 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 78381056 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.29 sec [bwa_aln_core] refine gapped alignments... 12.34 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 78643200 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.68 sec [bwa_aln_core] refine gapped alignments... 11.29 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 78905344 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 34.36 sec [bwa_aln_core] refine gapped alignments... 2.72 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 79167488 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.66 sec [bwa_aln_core] refine gapped alignments... 11.29 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 79429632 sequences have been processed. [bwa_read_seq] 2.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.47 sec [bwa_aln_core] refine gapped alignments... 2.67 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 79691776 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.77 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 79953920 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.26 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 80216064 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.28 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 80478208 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 80740352 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 81002496 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 81264640 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 81526784 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 81788928 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 82051072 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 82313216 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.27 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 82575360 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.44 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 82837504 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.27 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 83099648 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.27 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 83361792 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 83623936 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 83886080 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 84148224 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 84410368 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.65 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 84672512 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.29 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 84934656 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.27 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 85196800 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.28 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 85458944 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.28 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 85721088 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.27 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 85983232 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.28 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 86245376 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 86507520 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.24 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 86769664 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.29 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 87031808 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.29 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 87293952 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 87556096 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.34 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 87818240 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.29 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 88080384 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.29 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 88342528 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 88604672 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 88866816 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.69 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 89128960 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.34 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 89391104 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 89653248 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 89915392 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 90177536 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 90439680 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 90701824 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 90963968 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 91226112 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 91488256 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.41 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 91750400 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 92012544 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 92274688 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.75 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 92536832 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.69 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 92798976 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 93061120 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 93323264 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.30 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 93585408 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 93847552 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 94109696 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.55 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 94371840 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.81 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 94633984 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.78 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 94896128 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.06 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 95158272 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.01 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 95420416 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.34 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 95682560 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.38 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 95944704 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 96206848 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.14 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 96468992 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.76 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 96731136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.75 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 96993280 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.87 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 97255424 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.28 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 97517568 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.81 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 97779712 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.65 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 98041856 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.77 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 98304000 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 3.91 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 98566144 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.71 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 98828288 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.68 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 99090432 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.88 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 99352576 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.92 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 99614720 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.64 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 99876864 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.40 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 100139008 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.36 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 100401152 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.84 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 100663296 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.43 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 100925440 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.81 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 101187584 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.90 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.18 sec [bwa_aln_core] 101449728 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.88 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 101711872 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.75 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 101974016 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.62 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 102236160 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.51 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 102498304 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.28 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 102760448 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.00 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 103022592 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.46 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 103284736 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.69 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 103546880 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.16 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 103809024 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.09 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 104071168 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.01 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.18 sec [bwa_aln_core] 104333312 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.03 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 104595456 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.08 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 104857600 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.28 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 105119744 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.02 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 105381888 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.05 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 105644032 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.23 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 105906176 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.27 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 106168320 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.54 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 106430464 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.48 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 106692608 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.88 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 106954752 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.87 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 107216896 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.89 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 107479040 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.05 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 107741184 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.91 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 108003328 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.88 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 108265472 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.79 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 108527616 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.02 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 108789760 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.92 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 109051904 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.23 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 109314048 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.35 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 109576192 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.25 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 109838336 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.73 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 110100480 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.00 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 110362624 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.51 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 110624768 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.83 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 110886912 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.52 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 111149056 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 5.65 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 111411200 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.33 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 111673344 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.48 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 111935488 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.57 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 112197632 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.85 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 112459776 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.08 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 112721920 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.91 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 112984064 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.04 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 113246208 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.93 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 113508352 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.84 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 113770496 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.72 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.18 sec [bwa_aln_core] 114032640 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.90 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 114294784 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.94 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 114556928 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.05 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 114819072 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.00 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 115081216 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.74 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 115343360 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.29 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 115605504 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.17 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 115867648 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.38 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 116129792 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.53 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 116391936 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.82 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 116654080 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.04 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 116916224 sequences have been processed. [bwa_read_seq] 4.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.58 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 117178368 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.41 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 117440512 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.35 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 117702656 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.74 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 117964800 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.02 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 118226944 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.80 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 118489088 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.76 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 118751232 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 6.85 sec [bwa_aln_core] refine gapped alignments... 0.37 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 119013376 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.58 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 119275520 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.77 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 119537664 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.94 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 119799808 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.06 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 120061952 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.21 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.13 sec [bwa_aln_core] 120324096 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.23 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 120586240 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.63 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 120848384 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.01 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.18 sec [bwa_aln_core] 121110528 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.40 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 121372672 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.86 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.18 sec [bwa_aln_core] 121634816 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.86 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 121896960 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.77 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.17 sec [bwa_aln_core] 122159104 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.54 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 122421248 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.71 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 122683392 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.49 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 122945536 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.42 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 123207680 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.73 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 123469824 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.57 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.24 sec [bwa_aln_core] 123731968 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.72 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.18 sec [bwa_aln_core] 123994112 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.34 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 124256256 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.33 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.17 sec [bwa_aln_core] 124518400 sequences have been processed. [bwa_read_seq] 3.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.31 sec [bwa_aln_core] refine gapped alignments... 0.33 sec [bwa_aln_core] print alignments... 0.15 sec [bwa_aln_core] 124780544 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.62 sec [bwa_aln_core] refine gapped alignments... 0.34 sec [bwa_aln_core] print alignments... 0.16 sec [bwa_aln_core] 125042688 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.68 sec [bwa_aln_core] refine gapped alignments... 0.36 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 125304832 sequences have been processed. [bwa_read_seq] 4.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.57 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 125566976 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.00 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 125829120 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.09 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 126091264 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.41 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 126353408 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.30 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 126615552 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.16 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 126877696 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.68 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.20 sec [bwa_aln_core] 127139840 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.46 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 127401984 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.11 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 127664128 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.86 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 127926272 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 128188416 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.34 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 128450560 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.73 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 128712704 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.91 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 128974848 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.23 sec [bwa_aln_core] 129236992 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.51 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 129499136 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.75 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 129761280 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.18 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 130023424 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.89 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 130285568 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.22 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 130547712 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.98 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 130809856 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.93 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 131072000 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.17 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 131334144 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.15 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 131596288 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.22 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 131858432 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.22 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 132120576 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.18 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 132382720 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.43 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 132644864 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.53 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 132907008 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.02 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 133169152 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.24 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 133431296 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.56 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 133693440 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.82 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 133955584 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.15 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 134217728 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.44 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 134479872 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.38 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 134742016 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.26 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 135004160 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.89 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.22 sec [bwa_aln_core] 135266304 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.05 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 135528448 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.63 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 135790592 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.42 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 136052736 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 136314880 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 136577024 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 136839168 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 137101312 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 137363456 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 137625600 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 137887744 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 138149888 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 138412032 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.36 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 138674176 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 138936320 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 139198464 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.36 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 139460608 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 139722752 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.63 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 139984896 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.51 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 140247040 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.29 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 140509184 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 140771328 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.35 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 141033472 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 141295616 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 141557760 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.37 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.21 sec [bwa_aln_core] 141819904 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.32 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 142082048 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.37 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 142344192 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.40 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 142606336 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.44 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.25 sec [bwa_aln_core] 142868480 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.34 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 143130624 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.31 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 143392768 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.42 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 143654912 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.38 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 143917056 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.33 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 144179200 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.48 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 144441344 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.52 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 144703488 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.52 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 144965632 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.21 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 145227776 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.75 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 145489920 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.88 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 145752064 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.91 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 146014208 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.17 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 146276352 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.85 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 146538496 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.29 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 146800640 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.02 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 147062784 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.88 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 147324928 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.38 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 147587072 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.12 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 147849216 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.89 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 148111360 sequences have been processed. [bwa_read_seq] 3.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.76 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 148373504 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.75 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 148635648 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.84 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 148897792 sequences have been processed. [bwa_read_seq] 3.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.87 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 149159936 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.64 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 149422080 sequences have been processed. [bwa_read_seq] 3.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.72 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 149684224 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.54 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 149946368 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.45 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 150208512 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.10 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 150470656 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.82 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 150732800 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.85 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 150994944 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.63 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 151257088 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.64 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 151519232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.45 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 151781376 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.88 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 152043520 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.52 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 152305664 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.04 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 152567808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.51 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 152829952 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.99 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 153092096 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.17 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 153354240 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.14 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 153616384 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.11 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 153878528 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.16 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 154140672 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.14 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 154402816 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.11 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 154664960 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.07 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 154927104 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 155189248 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 155451392 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 155713536 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 155975680 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.68 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 156237824 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.68 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 156499968 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.69 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 156762112 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.60 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 157024256 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.60 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 157286400 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.59 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 157548544 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 157810688 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 158072832 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.37 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 158334976 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 158597120 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 17.58 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 158859264 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.04 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 159121408 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.65 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.28 sec [bwa_aln_core] 159383552 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.97 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 159645696 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.24 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 159907840 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.52 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.33 sec [bwa_aln_core] 160169984 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.52 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 160432128 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.80 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 160694272 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.71 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 160956416 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.75 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 161218560 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.23 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 161480704 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.12 sec [bwa_aln_core] refine gapped alignments... 0.55 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 161742848 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.68 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 162004992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.30 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 162267136 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.76 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 162529280 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.83 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 162791424 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.32 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 163053568 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.20 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 163315712 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.04 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 163577856 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.77 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 163840000 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.18 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 164102144 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.63 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 164364288 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.29 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 164626432 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.53 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 164888576 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.52 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 165150720 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.41 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 165412864 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.71 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 165675008 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 165937152 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.66 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 166199296 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.92 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 166461440 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.26 sec [bwa_aln_core] 166723584 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 166985728 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 167247872 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 167510016 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.77 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 167772160 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.75 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.27 sec [bwa_aln_core] 168034304 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.22 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 168296448 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.47 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 168558592 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 18.10 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 168820736 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.14 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 169082880 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.86 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 169345024 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.11 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 169607168 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.35 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 169869312 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.09 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.30 sec [bwa_aln_core] 170131456 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.07 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 170393600 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.95 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 170655744 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.82 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.29 sec [bwa_aln_core] 170917888 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.52 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 171180032 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.82 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 171442176 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.69 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 171704320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.81 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 171966464 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.68 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 172228608 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.69 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 172490752 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.54 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 172752896 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.61 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 173015040 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.59 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 173277184 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.72 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 173539328 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.69 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 173801472 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.76 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 174063616 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 8.97 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 174325760 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.81 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 174587904 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.23 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 174850048 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.59 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 175112192 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.99 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 175374336 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.09 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 175636480 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.44 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 175898624 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.61 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 176160768 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.68 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 176422912 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.53 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 176685056 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.24 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 176947200 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.37 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 177209344 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.64 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 177471488 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.20 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 177733632 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.69 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.31 sec [bwa_aln_core] 177995776 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.43 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 178257920 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.82 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 178520064 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.45 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 178782208 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.35 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 179044352 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.15 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 179306496 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.20 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 179568640 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.45 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 179830784 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.47 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 180092928 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.56 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 180355072 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.71 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 180617216 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.76 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 180879360 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.06 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 181141504 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.01 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 181403648 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.02 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 181665792 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.66 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 181927936 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.68 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 182190080 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.59 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 182452224 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 182714368 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.69 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 182976512 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.72 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 183238656 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 183500800 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.69 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 183762944 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 184025088 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 184287232 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.67 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 184549376 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.65 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 184811520 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.55 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 185073664 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.65 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 185335808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.41 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 185597952 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.38 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.34 sec [bwa_aln_core] 185860096 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.25 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 186122240 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.70 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 186384384 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.45 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 186646528 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.76 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.36 sec [bwa_aln_core] 186908672 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.68 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 187170816 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.37 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 187432960 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.33 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 187695104 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.45 sec [bwa_aln_core] refine gapped alignments... 0.40 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 187957248 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.73 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 188219392 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.63 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 188481536 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.41 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 188743680 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.84 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 189005824 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.80 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 189267968 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.03 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 189530112 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.81 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 189792256 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.60 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 190054400 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.00 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 190316544 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.94 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 190578688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.82 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 190840832 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.84 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 191102976 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.00 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 191365120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.07 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 191627264 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.04 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 191889408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.11 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 192151552 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.10 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 192413696 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.09 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 192675840 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.78 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 192937984 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.41 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 193200128 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.29 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 193462272 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.47 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 193724416 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.89 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 193986560 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.27 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 194248704 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.31 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 194510848 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.20 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 194772992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.37 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 195035136 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.36 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 195297280 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.24 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 195559424 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 4.38 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 195821568 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.79 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 196083712 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.79 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 196345856 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.78 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 196608000 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.82 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 196870144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.76 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 197132288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.75 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 197394432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.76 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 197656576 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.76 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 197918720 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.65 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 198180864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 22.44 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 198443008 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.61 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 198705152 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.56 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 198967296 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.53 sec [bwa_aln_core] refine gapped alignments... 0.85 sec [bwa_aln_core] print alignments... 0.38 sec [bwa_aln_core] 199229440 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.79 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 199491584 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.42 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 199753728 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.84 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 200015872 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.57 sec [bwa_aln_core] refine gapped alignments... 5.41 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 200278016 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.80 sec [bwa_aln_core] refine gapped alignments... 6.99 sec [bwa_aln_core] print alignments... 0.32 sec [bwa_aln_core] 200540160 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.47 sec [bwa_aln_core] refine gapped alignments... 6.95 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 200802304 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.87 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 201064448 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.50 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 201326592 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 51.15 sec [bwa_aln_core] refine gapped alignments... 0.44 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 201588736 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 50.94 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 201850880 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 40.57 sec [bwa_aln_core] refine gapped alignments... 4.33 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 202113024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.69 sec [bwa_aln_core] refine gapped alignments... 10.50 sec [bwa_aln_core] print alignments... 0.37 sec [bwa_aln_core] 202375168 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.70 sec [bwa_aln_core] refine gapped alignments... 4.25 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 202637312 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.63 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 202899456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 59.98 sec [bwa_aln_core] refine gapped alignments... 1.44 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 203161600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 69.51 sec [bwa_aln_core] refine gapped alignments... 10.30 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 203423744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.99 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 203685888 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.99 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 203948032 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.83 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 204210176 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.86 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 204472320 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.39 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.35 sec [bwa_aln_core] 204734464 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 23.99 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 204996608 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.49 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 205258752 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.06 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 205520896 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.04 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 205783040 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.00 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 206045184 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 28.60 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 206307328 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.12 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 206569472 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.96 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 206831616 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.13 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 207093760 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 7.78 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 207355904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 207618048 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.79 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 207880192 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.78 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 208142336 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.62 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 208404480 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.64 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 208666624 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.68 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 208928768 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.99 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 209190912 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.95 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 209453056 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.93 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 209715200 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 12.72 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 209977344 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 210239488 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 210501632 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.75 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 210763776 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 211025920 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.74 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 211288064 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.70 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 211550208 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.73 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 211812352 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.82 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 212074496 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.79 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 212336640 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.80 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 212598784 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.76 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 212860928 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.78 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 213123072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.79 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 213385216 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.81 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 213647360 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.80 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 213909504 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 2.80 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 214171648 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 20.97 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 214433792 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.63 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 214695936 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.00 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 214958080 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.23 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 215220224 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.85 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 215482368 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.76 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 215744512 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.31 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 216006656 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.52 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 216268800 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.26 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 216530944 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.52 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 216793088 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.39 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 217055232 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.86 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 217317376 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.29 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 217579520 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.08 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 217841664 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.68 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.44 sec [bwa_aln_core] 218103808 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.52 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 218365952 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.31 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 218628096 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.24 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 218890240 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.47 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 219152384 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.16 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 219414528 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.23 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 219676672 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.96 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.39 sec [bwa_aln_core] 219938816 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 13.87 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 220200960 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.22 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 220463104 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 14.24 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 220725248 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.36 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 220987392 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.32 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.45 sec [bwa_aln_core] 221249536 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 16.93 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.43 sec [bwa_aln_core] 221511680 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 15.42 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 221773824 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.50 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.41 sec [bwa_aln_core] 222035968 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.06 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 222298112 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.94 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.46 sec [bwa_aln_core] 222560256 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.70 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 222822400 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 10.79 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 223084544 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 11.26 sec [bwa_aln_core] refine gapped alignments... 0.43 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 223346688 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.19 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 223608832 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.12 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.40 sec [bwa_aln_core] 223870976 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.04 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 224133120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 21.67 sec [bwa_aln_core] refine gapped alignments... 0.41 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 224395264 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.89 sec [bwa_aln_core] refine gapped alignments... 0.45 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 224657408 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.62 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 224919552 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 38.08 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.42 sec [bwa_aln_core] 225181696 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 32.65 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 225443840 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 39.92 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 225705984 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.80 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 225968128 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.13 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 226230272 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.97 sec [bwa_aln_core] refine gapped alignments... 0.46 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 226492416 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.59 sec [bwa_aln_core] refine gapped alignments... 0.42 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 226754560 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 42.43 sec [bwa_aln_core] refine gapped alignments... 0.35 sec [bwa_aln_core] print alignments... 0.14 sec [bwa_aln_core] 226802161 sequences have been processed. [main] Version: 0.7.13-r1126 [main] CMD: bwa samse /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF5_allReps.fastq.gz [main] Real time: 27056.639 sec; CPU: 26572.328 sec | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 97
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 105
if [[ 0 > 0 ]]; then \
sambamba sort -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
samtools view -F 1804 -Su /dev/stdin | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.bam | \
sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.filt.bam; \
fi
# SYS command. line 116
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 6397 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 349
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 353
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 354
export MAX_JAVA_MEM="12G"
# SYS command. line 359
if [ -f "${PICARDROOT}/picard.jar" ]; then \
MARKDUP="${PICARDROOT}/picard.jar MarkDuplicates"; \
elif [ -f "${PICARDROOT}/MarkDuplicates.jar" ]; then \
MARKDUP="${PICARDROOT}/MarkDuplicates.jar"; \
elif [ $(which picard 2> /dev/null | wc -l || echo) == "1" ]; then \
MARKDUP="$(ls $(dirname $(which picard))/../share/picard*/MarkDuplicates.jar 2> /dev/null || echo)"; \
fi
# SYS command. line 368
if [ -f "${MARKDUP}" ]; then \
java -Xmx4G -jar ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 21959 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1 [Thu Sep 29 06:17:52 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Thu Sep 29 06:17:52 PDT 2016] Executing as imk1@kadru on Linux 4.4.0-22-generic amd64; OpenJDK 64-Bit Server VM 1.6.0-77-b77; Picard version: 1.97(Unversioned directory) INFO 2016-09-29 06:17:52 MarkDuplicates Start of doWork freeMemory: 255390224; totalMemory: 257294336; maxMemory: 3817799680 INFO 2016-09-29 06:17:52 MarkDuplicates Reading input file and constructing read end information. INFO 2016-09-29 06:17:52 MarkDuplicates Will retain up to 15149998 data points before spilling to disk. WARNING 2016-09-29 06:17:53 AbstractDuplicateFindingAlgorithm Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'SRR836479.18055944'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. INFO 2016-09-29 06:18:01 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 7s. Last read position: chr1:37,077,533 INFO 2016-09-29 06:18:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:07 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 5s. Last read position: chr1:63,993,193 INFO 2016-09-29 06:18:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:12 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 4s. Last read position: chr1:92,304,608 INFO 2016-09-29 06:18:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:15 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:125,915,200 INFO 2016-09-29 06:18:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:21 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 5s. Last read position: chr1:149,484,697 INFO 2016-09-29 06:18:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:25 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr1:171,681,341 INFO 2016-09-29 06:18:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:28 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr2:3,721,989 INFO 2016-09-29 06:18:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:32 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 4s. Last read position: chr2:30,270,436 INFO 2016-09-29 06:18:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:34 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr2:53,133,310 INFO 2016-09-29 06:18:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:37 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr2:78,010,629 INFO 2016-09-29 06:18:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:42 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 4s. Last read position: chr2:103,681,555 INFO 2016-09-29 06:18:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr2:127,832,814 INFO 2016-09-29 06:18:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:47 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr2:154,528,262 INFO 2016-09-29 06:18:47 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:50 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr2:181,500,175 INFO 2016-09-29 06:18:50 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:18:56 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 5s. Last read position: chr3:37,474,838 INFO 2016-09-29 06:18:56 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:05 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 9s. Last read position: chr3:67,558,360 INFO 2016-09-29 06:19:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:07 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr3:93,429,963 INFO 2016-09-29 06:19:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:10 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr3:116,419,320 INFO 2016-09-29 06:19:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:13 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr3:140,917,592 INFO 2016-09-29 06:19:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:16 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr4:11,726,707 INFO 2016-09-29 06:19:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:18 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr4:44,325,198 INFO 2016-09-29 06:19:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:20 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr4:74,326,164 INFO 2016-09-29 06:19:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:23 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: chr4:105,796,924 INFO 2016-09-29 06:19:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:25 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr4:130,307,873 INFO 2016-09-29 06:19:25 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:27 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr4:155,163,122 INFO 2016-09-29 06:19:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:32 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 4s. Last read position: chr5:32,403,625 INFO 2016-09-29 06:19:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:34 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr5:63,258,907 INFO 2016-09-29 06:19:34 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:36 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr5:91,624,535 INFO 2016-09-29 06:19:36 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:39 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr5:118,480,765 INFO 2016-09-29 06:19:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:42 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr5:143,525,664 INFO 2016-09-29 06:19:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:53 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 11s. Last read position: chr6:24,299,746 INFO 2016-09-29 06:19:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr6:51,208,178 INFO 2016-09-29 06:19:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:19:58 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr6:82,908,608 INFO 2016-09-29 06:19:58 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:01 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr6:109,896,790 INFO 2016-09-29 06:20:01 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:05 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr6:136,136,662 INFO 2016-09-29 06:20:05 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:06 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr7:25,514,242 INFO 2016-09-29 06:20:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:08 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr7:60,902,961 INFO 2016-09-29 06:20:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:11 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr7:89,661,525 INFO 2016-09-29 06:20:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr7:114,591,097 INFO 2016-09-29 06:20:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:16 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr7:141,318,973 INFO 2016-09-29 06:20:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:18 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr8:33,944,063 INFO 2016-09-29 06:20:18 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:20 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr8:66,447,699 INFO 2016-09-29 06:20:20 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:24 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: chr8:92,314,129 INFO 2016-09-29 06:20:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:29 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 5s. Last read position: chr8:120,595,052 INFO 2016-09-29 06:20:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:31 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr9:22,642,727 INFO 2016-09-29 06:20:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:38 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 7s. Last read position: chr9:53,525,047 INFO 2016-09-29 06:20:38 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:41 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr9:75,435,996 INFO 2016-09-29 06:20:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:43 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr9:103,364,498 INFO 2016-09-29 06:20:43 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:46 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr10:7,793,827 INFO 2016-09-29 06:20:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:49 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr10:35,070,259 INFO 2016-09-29 06:20:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:53 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 3s. Last read position: chr10:61,309,053 INFO 2016-09-29 06:20:53 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:55 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr10:85,041,175 INFO 2016-09-29 06:20:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:20:57 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr10:110,752,986 INFO 2016-09-29 06:20:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:00 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr11:6,294,322 INFO 2016-09-29 06:21:00 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:02 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr11:35,487,986 INFO 2016-09-29 06:21:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:06 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr11:61,876,238 INFO 2016-09-29 06:21:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:08 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr11:83,964,571 INFO 2016-09-29 06:21:08 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:10 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr11:104,362,366 INFO 2016-09-29 06:21:10 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:12 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr12:8,236,612 INFO 2016-09-29 06:21:12 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:15 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr12:45,247,117 INFO 2016-09-29 06:21:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:24 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 9s. Last read position: chr12:76,310,237 INFO 2016-09-29 06:21:24 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:26 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr12:101,029,207 INFO 2016-09-29 06:21:26 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:28 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr13:14,628,751 INFO 2016-09-29 06:21:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:31 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr13:41,998,061 INFO 2016-09-29 06:21:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:33 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr13:71,312,277 INFO 2016-09-29 06:21:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:35 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr13:97,914,275 INFO 2016-09-29 06:21:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:37 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr14:10,308,600 INFO 2016-09-29 06:21:37 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:39 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr14:45,845,309 INFO 2016-09-29 06:21:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:41 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr14:72,699,126 INFO 2016-09-29 06:21:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:44 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 3s. Last read position: chr14:101,267,380 INFO 2016-09-29 06:21:44 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:46 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr15:8,563,305 INFO 2016-09-29 06:21:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:49 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr15:44,841,433 INFO 2016-09-29 06:21:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:52 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr15:75,799,718 INFO 2016-09-29 06:21:52 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:55 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr15:99,873,470 INFO 2016-09-29 06:21:55 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:21:57 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr16:24,703,903 INFO 2016-09-29 06:21:57 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:07 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 9s. Last read position: chr16:49,690,769 INFO 2016-09-29 06:22:07 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:09 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr16:76,952,004 INFO 2016-09-29 06:22:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:11 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr17:9,745,532 INFO 2016-09-29 06:22:11 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:13 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr17:34,975,906 INFO 2016-09-29 06:22:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:15 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr17:61,326,663 INFO 2016-09-29 06:22:15 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:17 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr17:87,511,143 INFO 2016-09-29 06:22:17 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:19 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr18:31,341,678 INFO 2016-09-29 06:22:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:21 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr18:58,497,007 INFO 2016-09-29 06:22:21 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:23 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr18:85,358,572 INFO 2016-09-29 06:22:23 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:27 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 3s. Last read position: chr19:25,519,787 INFO 2016-09-29 06:22:27 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:28 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr19:50,158,038 INFO 2016-09-29 06:22:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:31 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chrX:52,472,721 INFO 2016-09-29 06:22:31 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:33 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chrX:116,422,997 INFO 2016-09-29 06:22:33 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:41 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 7s. Last read position: GL456392.1:22,710 INFO 2016-09-29 06:22:41 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 06:22:41 MarkDuplicates Read 89030412 records. 0 pairs never matched. INFO 2016-09-29 06:22:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 2365030496; totalMemory: 2452684800; maxMemory: 3817799680 INFO 2016-09-29 06:22:46 MarkDuplicates Will retain up to 119306240 duplicate indices before spilling to disk. INFO 2016-09-29 06:22:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-09-29 06:22:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-09-29 06:23:07 MarkDuplicates Sorting list of duplicate records. INFO 2016-09-29 06:23:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 2136673104; totalMemory: 3116957696; maxMemory: 3817799680 INFO 2016-09-29 06:23:09 MarkDuplicates Marking 29539370 records as duplicates. INFO 2016-09-29 06:23:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-09-29 06:24:40 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 90s. Last read position: chr2:78,010,629 INFO 2016-09-29 06:26:10 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:03:01s. Time for last 10,000,000: 90s. Last read position: chr4:11,726,707 INFO 2016-09-29 06:27:42 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:04:32s. Time for last 10,000,000: 91s. Last read position: chr5:143,525,664 INFO 2016-09-29 06:29:13 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:06:03s. Time for last 10,000,000: 91s. Last read position: chr7:141,318,973 INFO 2016-09-29 06:30:45 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:07:35s. Time for last 10,000,000: 91s. Last read position: chr10:35,070,259 INFO 2016-09-29 06:32:15 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:09:06s. Time for last 10,000,000: 90s. Last read position: chr12:45,247,117 INFO 2016-09-29 06:33:47 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:10:37s. Time for last 10,000,000: 91s. Last read position: chr14:101,267,380 INFO 2016-09-29 06:35:19 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:12:09s. Time for last 10,000,000: 91s. Last read position: chr17:61,326,663 INFO 2016-09-29 06:36:42 MarkDuplicates Before output close freeMemory: 3184136672; totalMemory: 3213950976; maxMemory: 3817799680 INFO 2016-09-29 06:36:42 MarkDuplicates After output close freeMemory: 3184070296; totalMemory: 3213885440; maxMemory: 3817799680 [Thu Sep 29 06:36:42 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 18.83 minutes. Runtime.totalMemory()=3213885440 | ||||||||||||||||||||||||||||||||||||||||
|
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# SYS command. line 146
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 150
samtools view -F 1804 -b /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.bam
# SYS command. line 153
sambamba index -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.bam
# SYS command. line 155
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.dupmark.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$6}' | \
grep -v 'chrM' | sort | uniq -c | \
awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{m1_m2=-1.0; if(m2>0) m1_m2=m1/m2; printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1_m2}' > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.pbc.qc
# SYS command. line 169
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 7931 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 506
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 509
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 9326 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 43
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 46
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz | \
grep -v "chrM" | shuf -n 15000000 | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.15M.tagAlign.gz
# SYS command. line 49
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 6728 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 249
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 252
nlines=$( zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz | wc -l )
# SYS command. line 253
nlines=$(( (nlines + 1) / 2 ))
# SYS command. line 257
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz | shuf | split -d -l $((nlines)) - /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr1/ZF5_allReps.nodup.
# SYS command. line 260
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr1/ZF5_allReps.nodup.00 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr1/ZF5_allReps.nodup.pr1.tagAlign.gz
# SYS command. line 261
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr1/ZF5_allReps.nodup.00
# SYS command. line 262
gzip -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr1/ZF5_allReps.nodup.01 > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr2/ZF5_allReps.nodup.pr2.tagAlign.gz
# SYS command. line 263
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/pseudo_reps/rep1/pr1/ZF5_allReps.nodup.01
# SYS command. line 265
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 9622 (process ID) old priority 0, new priority 10 --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 207
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 210
if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 216
Rscript ${RUN_SPP} -rf \
-c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.15M.tagAlign.gz -p=4 \
-filtchr=chrM -savp=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.plot.pdf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.qc
# SYS command. line 219
sed -r 's/,[^\t]+//g' /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.qc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.qc.tmp
# SYS command. line 220
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.qc.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.qc
# SYS command. line 222
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
23442 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.15M.tagAlign.gz
Control data: NA
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift NA
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 4
FDR threshold: 0.01
NumPeaks Threshold: NA
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1
narrowPeak output file name: NA
regionPeak output file name: NA
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.plot.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/qc/rep1/ZF5_allReps.nodup.15M.cc.qc
Overwrite files?: TRUE
Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.15M.tagAlign.gz
opened /tmp/9797.1.q/RtmpghFJJt/ZF5_allReps.nodup.15M.tagAlign5bd67226ec0e
done. read 15000000 fragments
ChIP data read length 50
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1947552
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.206627460827475,0.20606715774499,0.202506584363655
Top 3 estimates for fragment length 95,115,215
Window half size 590
Phantom peak location 55
Phantom peak Correlation 0.2039394
Normalized Strand cross-correlation coefficient (NSC) 1.06096
Relative Strand Cross correlation Coefficient (RSC) 1.29269
Phantom Peak Quality Tag 1
null device
1
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
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# SYS command. line 56
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 59
if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 63
Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1 -speak=95 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Error message--------------------
Task disappeared from cluster's queue. Task or node failure?
--------------------Stdout--------------------
6819 (process ID) old priority 0, new priority 10
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 95
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/peak/spp/rep1/ZF5_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/rep1/ZF5_allReps.nodup.tagAlign.gz
opened /tmp/9799.1.q/Rtmp8RncIw/ZF5_allReps.nodup.tagAlign1ae51dfc7453
done. read 59491042 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out/align/ctl1/mousePrimaryBCellInput.nodup.tagAlign.gz
opened /tmp/9799.1.q/Rtmp8RncIw/mousePrimaryBCellInput.nodup.tagAlign1ae57a061900
done. read 15331612 fragments
Control data read length 36
Calculating peak characteristics
Minimum cross-correlation value 0.472235
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.500991373593797
Top 3 estimates for fragment length 95
Window half size 595
Phantom peak location 55
Phantom peak Correlation 0.4946806
Normalized Strand cross-correlation coefficient (NSC) 1.060894
Relative Strand Cross correlation Coefficient (RSC) 1.28116
Phantom Peak Quality Tag 1
null device
1
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.2798708
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
|
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| bool | allowEmpty | false |
| string[] | args | [-title, ZF5, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF5/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/ZF5_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.fastq.gz, $] |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DISPLAY | localhost:19.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/keras |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_eHVWt0 |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5 |
| string | PERL_MB_OPT | --install_base \"/users/imk1/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=/users/imk1/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5 |
| string | programName | chipseq.bds |
| string | programPath | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
| string | PWD | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF5 |
| string | PYTHONPATH | /software/python_anaconda/2.2.0/bin/python:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/ |
| string | queue | |
| int | retry | 0 |
| string | RULEFITBASE | /srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/ |
| string | SGE_CELL | default |
| string | SGE_ROOT | /var/lib/gridengine |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 58475 22 |
| string | SSH_CONNECTION | 171.65.77.8 58475 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/38 |
| string | STY | 4476.ZF5.BDS |
| string | system | sge |
| int | T | 1099511627776 |
| string | TERM | screen |
| string | TERMCAP | SC|screen|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#24:co#80:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:Km=\\E[M:k0=\\E[10~:k1=\\EOP:\\\n\t:k2=\\EOQ:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:\\\n\t:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:kd=\\EOB:kr=\\EOC:kl=\\EOD: |
| int | timeout | -1 |
| string | USER | imk1 |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/ |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1048 |
| string | XDG_SESSION_ID | 418 |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |