| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20160929_154250_022 |
| Start time | 2016-09-29 15:42:50 |
| Run time | 05:03:55.326 |
| Tasks executed | 8 |
| Tasks failed | 1 |
| Tasks failed names | bwa_sam rep1 |
| Arguments* | [-title, R339W, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/R339W_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz, $] |
| System* | sge |
| Cpus* | -1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_41 | thread_Root | chipseq.bds.20160929_154250_022_parallel_41/task.align_bwa.bwa_aln_rep1.line_108.id_11 chipseq.bds.20160929_154250_022_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13 |
| thread_42 | thread_Root | chipseq.bds.20160929_154250_022_parallel_42/task.align_bwa.bwa_aln_ctl1.line_108.id_10 chipseq.bds.20160929_154250_022_parallel_42/task.align_bwa.bwa_sam_ctl1.line_140.id_12 chipseq.bds.20160929_154250_022_parallel_42/task.postalign_bam.dedup_bam_1_ctl1.line_95.id_14 chipseq.bds.20160929_154250_022_parallel_42/task.postalign_bam.markdup_bam_picard_ctl1.line_347.id_15 chipseq.bds.20160929_154250_022_parallel_42/task.postalign_bam.dedup_bam_2_ctl1.line_144.id_16 chipseq.bds.20160929_154250_022_parallel_42/task.postalign_bam.bam_to_tag_ctl1.line_504.id_17 |
| 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 1 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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-------------------- 40225 (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] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.16 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.46 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.47 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.25 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.41 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.27 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.24 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.10 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.84 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.58 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.81 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.01 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.85 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.62 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.10 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.83 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.80 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.17 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.92 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.64 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.30 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.37 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.11 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 55.13 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.46 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.47 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.58 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.19 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... 49.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.10 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.84 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.65 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.93 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.64 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.45 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 56.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 53.03 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.33 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.04 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.69 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.84 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.82 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.94 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.10 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 57.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.50 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 58.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.20 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.43 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.87 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.36 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.69 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.61 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.88 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.73 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.81 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.17 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.66 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.22 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.23 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.67 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.97 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 7.33 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 32022635 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/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz [main] Real time: 6322.500 sec; CPU: 6326.176 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 4 /mnt/data/bds_pipeline_genome_data/mm10/bwa_index/GRCm38.p4.genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/R339W_allReps.fastq.gz > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_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-------------------- 4339 (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] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.41 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.15 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.62 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.26 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.68 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.90 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.90 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.39 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.01 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.01 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.91 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.14 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.89 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.56 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.52 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.87 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.66 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.48 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.83 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.39 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.95 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.16 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.54 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.30 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.09 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.18 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.37 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.66 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.53 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 29.92 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.04 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.56 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.96 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.82 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.72 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.41 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.69 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.44 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.28 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.34 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.56 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.18 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.29 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.98 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.76 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.76 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.32 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.78 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.16 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32243712 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.68 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32505856 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 32768000 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 33030144 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 33292288 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.55 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 33554432 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 33816576 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 34078720 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 34340864 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 34603008 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 34865152 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 35127296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.56 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 35389440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 35651584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 35913728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 36175872 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.55 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 36438016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.29 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 36700160 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.40 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 36962304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 37224448 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 37486592 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.91 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 37748736 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.60 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 38010880 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 38273024 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.82 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 38535168 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.44 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 38797312 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 39059456 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 39321600 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.78 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 39583744 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.04 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 39845888 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.71 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 40108032 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.71 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 40370176 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.31 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 40632320 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.10 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 40894464 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.37 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 41156608 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 41418752 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.96 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 41680896 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.20 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 41943040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 42205184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.03 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 42467328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 42729472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.63 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 42991616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.99 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 43253760 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 30.84 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 43515904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.01 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 43778048 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.35 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 44040192 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.05 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 44302336 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.94 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 44564480 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.97 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 44826624 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 45088768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.12 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 45350912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 45613056 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 45875200 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.49 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46137344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.83 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46399488 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.30 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 46661632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.54 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 46923776 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.86 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47185920 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.91 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47448064 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 47710208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.23 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 47972352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.02 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48234496 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.60 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48496640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.22 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 48758784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.19 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 49020928 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 49283072 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.25 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 49545216 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.87 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 49807360 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.67 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 50069504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 50331648 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.27 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 50593792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.42 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 50855936 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.13 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 51118080 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.48 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 51380224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.11 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 51642368 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.59 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 51904512 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.71 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 52166656 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.86 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 52428800 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.19 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 52690944 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.17 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 52953088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.71 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 53215232 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 53477376 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.77 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 53739520 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 54001664 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.94 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 54263808 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.49 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 54525952 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.51 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 54788096 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 55050240 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.71 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 55312384 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.21 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 55574528 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.45 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 55836672 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.73 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 56098816 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.82 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 56360960 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.32 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 56623104 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 56885248 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 57147392 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.66 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 57409536 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.39 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 57671680 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.70 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 57933824 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.20 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 58195968 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.56 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 58458112 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.61 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 58720256 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 58982400 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 59244544 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 59506688 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.22 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 59768832 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.92 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 60030976 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.16 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 60293120 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 60555264 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 60817408 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 61079552 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 61341696 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.28 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 61603840 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 61865984 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 62128128 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.77 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 62390272 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.07 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 62652416 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.68 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 62914560 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.93 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 63176704 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 63438848 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.17 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 63700992 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 63963136 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 64225280 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.46 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 64487424 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 64749568 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 65011712 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 65273856 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 65536000 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 65798144 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66060288 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 66322432 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.11 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 66584576 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 66846720 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 67108864 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.24 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 67371008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 67633152 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.26 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 67895296 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 68157440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 68419584 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 68681728 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 68943872 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 69206016 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 69468160 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 69730304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.95 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 69992448 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.53 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 70254592 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 70516736 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 70778880 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.25 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 71041024 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 71303168 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 71565312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.18 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 71827456 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 72089600 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.31 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 72351744 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 72613888 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 72876032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 73138176 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 73400320 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 73662464 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 73924608 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 74186752 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 74448896 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 74711040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.16 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 74973184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 75235328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 75497472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 75759616 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 76021760 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 76283904 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.36 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 76546048 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.50 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 76808192 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 77070336 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 77332480 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.32 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 77594624 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 77856768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78118912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78381056 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 78643200 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.39 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 78905344 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 79167488 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 79429632 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 79691776 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.94 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 79953920 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 80216064 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 80478208 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 80740352 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 47.49 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 81002496 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 48.88 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 81264640 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.00 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 81526784 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.63 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 81788928 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 82051072 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 82313216 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 82575360 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 82837504 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.25 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 83099648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.22 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 83361792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.42 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 83623936 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 83886080 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.86 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 84148224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.24 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 84410368 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.50 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 84672512 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 84934656 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 85196800 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.77 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 85458944 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.05 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 85721088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.90 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 85983232 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 86245376 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.83 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 86507520 sequences have been processed. [bwa_read_seq] 0.5% 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] 86769664 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 87031808 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 87293952 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.17 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 87556096 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.50 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 87818240 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 88080384 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 88342528 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.38 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 88604672 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.97 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 88866816 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 89128960 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 89391104 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.54 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 89653248 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.24 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 89915392 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.71 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 90177536 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.30 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 90439680 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 90701824 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.94 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 90963968 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.52 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 91226112 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.89 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 91488256 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 91750400 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 92012544 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 92274688 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 92536832 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.57 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 92798976 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.66 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 93061120 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 93323264 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 93585408 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 93847552 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 94109696 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 94371840 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 94633984 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.21 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 94896128 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 95158272 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 95420416 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 95682560 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 95944704 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.17 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 96206848 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 96468992 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.83 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 96731136 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 96993280 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.01 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 97255424 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.94 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 97517568 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 97779712 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.00 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 98041856 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 98304000 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 98566144 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 98828288 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 99090432 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 99352576 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 99614720 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 99876864 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 100139008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 100401152 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 100663296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 100925440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101187584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.71 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 101449728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101711872 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 101974016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.89 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 102236160 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 102498304 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.35 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 102760448 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 103022592 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 103284736 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 103546880 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 103809024 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 104071168 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 104333312 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.75 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 104595456 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.17 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 104857600 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.94 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 105119744 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.72 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 105381888 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 105644032 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 105906176 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 106168320 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 106430464 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.36 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 106692608 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 106954752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 107216896 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.69 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 107479040 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.95 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 107741184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.19 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 108003328 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 108265472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 108527616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.65 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 108789760 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 109051904 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 109314048 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.08 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 109576192 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 109838336 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.83 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 110100480 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.88 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 110362624 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 110624768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 110886912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 111149056 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 111411200 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.71 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 111673344 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.32 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 111935488 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 112197632 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.85 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 112459776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 112721920 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 112984064 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 113246208 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 113508352 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.21 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 113770496 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 114032640 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 114294784 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.62 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 114556928 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.22 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 114819072 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.50 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 115081216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 115343360 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 115605504 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.65 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 115867648 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 116129792 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.73 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 116391936 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 116654080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.81 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 116916224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.43 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 117178368 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 117440512 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 117702656 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.74 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 117964800 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.54 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 118226944 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 118489088 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 118751232 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 119013376 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 119275520 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 119537664 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.51 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 119799808 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 120061952 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.91 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 120324096 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 120586240 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 120848384 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.65 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 121110528 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 121372672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.67 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 121634816 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.26 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 121896960 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.63 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 122159104 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 122421248 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.90 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 122683392 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.64 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 122945536 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.07 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 123207680 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.06 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 123469824 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 123731968 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 123994112 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 124256256 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 124518400 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 124780544 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 125042688 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 125304832 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 125566976 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 125829120 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 126091264 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.51 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 126353408 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 126615552 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 126877696 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 127139840 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 127401984 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.26 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 127664128 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.46 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 127926272 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.35 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 128188416 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 128450560 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.08 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 128712704 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 128974848 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 129236992 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 129499136 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.65 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 129761280 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.77 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 130023424 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.06 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 130285568 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.52 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 130547712 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.75 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 130809856 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 131072000 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 131334144 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 131596288 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 131858432 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.05 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 132120576 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 132382720 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.59 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 132644864 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.14 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 132907008 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 133169152 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 133431296 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 133693440 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 133955584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 134217728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.64 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 134479872 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 134742016 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 135004160 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 135266304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 135528448 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 135790592 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 136052736 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.23 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 136314880 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 136577024 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.94 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 136839168 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.03 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 137101312 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.52 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 137363456 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 137625600 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.21 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 137887744 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.62 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 138149888 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 138412032 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 138674176 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.22 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 138936320 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 139198464 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.74 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 139460608 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 139722752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 139984896 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 140247040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.00 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 140509184 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.24 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 140771328 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 141033472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 141295616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 141557760 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.85 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 141819904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 142082048 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 142344192 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.00 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 142606336 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.21 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 142868480 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 143130624 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 143392768 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.37 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 143654912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 143917056 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 144179200 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 144441344 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.14 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 144703488 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 144965632 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 145227776 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 145489920 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 145752064 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.09 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 146014208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.80 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 146276352 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 146538496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 146800640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 147062784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 147324928 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 147587072 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.01 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 147849216 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 148111360 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 148373504 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 148635648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.25 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 148897792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149159936 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149422080 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.77 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 149684224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 149946368 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 150208512 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 150470656 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.03 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 150732800 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.30 sec [bwa_aln_core] write to the disk... 0.11 sec [bwa_aln_core] 150994944 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.31 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 151257088 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.80 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 151519232 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.07 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 151781376 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 152043520 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.53 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 152305664 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.75 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 152567808 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.48 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 152829952 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.50 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 153092096 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.55 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 153354240 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 54.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 153616384 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 153878528 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 154140672 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 154402816 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 154664960 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.42 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 154927104 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.64 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 155189248 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 155451392 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 155713536 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 155975680 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.14 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 156237824 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.63 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 156499968 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 156762112 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 157024256 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 157286400 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 157548544 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 157810688 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.90 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 158072832 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.17 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 158334976 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.24 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 158597120 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 158859264 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.44 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 159121408 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 159383552 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 159645696 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 159907840 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 160169984 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 160432128 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 160694272 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.60 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 160956416 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 161218560 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 161480704 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.98 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 161742848 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.30 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 162004992 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 162267136 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 162529280 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 162791424 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 163053568 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 163315712 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 163577856 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 163840000 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 164102144 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 164364288 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 164626432 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 164888576 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 165150720 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 165412864 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.63 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... 35.29 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... 35.62 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 166199296 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 166461440 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 166723584 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 166985728 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.99 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 167247872 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.40 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 167510016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 167772160 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 168034304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 168296448 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 168558592 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.89 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 168820736 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 169082880 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.58 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 169345024 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 169607168 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 169869312 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.36 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 170131456 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.62 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 170393600 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 170655744 sequences have been processed. [bwa_read_seq] 0.5% 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] 170917888 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 171180032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.00 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 171442176 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 171704320 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.43 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 171966464 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 172228608 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 172490752 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 172752896 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 173015040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.13 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 173277184 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 173539328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 173801472 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 174063616 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 174325760 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 174587904 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.98 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 174850048 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 175112192 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 175374336 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 175636480 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.59 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 175898624 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 176160768 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 176422912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 176685056 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 176947200 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 177209344 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.41 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 177471488 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 177733632 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 177995776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 178257920 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 178520064 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.41 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 178782208 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 179044352 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 179306496 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.56 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 179568640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 179830784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 180092928 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 180355072 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 180617216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.29 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 180879360 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 181141504 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 181403648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.84 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 181665792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 181927936 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 182190080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 182452224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.77 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 182714368 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 182976512 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 183238656 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.01 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 183500800 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 183762944 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 184025088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.44 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184287232 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184549376 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.46 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 184811520 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 185073664 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 49.83 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 185335808 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 51.33 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 185597952 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 52.61 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 185860096 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 50.97 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 186122240 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 186384384 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 186646528 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.91 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 186908672 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 187170816 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.92 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 187432960 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 187695104 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 187957248 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 188219392 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 188481536 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.61 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 188743680 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.58 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 189005824 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.23 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 189267968 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 189530112 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 189792256 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.10 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 190054400 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 190316544 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.16 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 190578688 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 190840832 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.82 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 191102976 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.78 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 191365120 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.10 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 191627264 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.13 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 191889408 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 192151552 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 192413696 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 192675840 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 192937984 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.37 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 193200128 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 193462272 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.08 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 193724416 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 193986560 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.45 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 194248704 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.66 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 194510848 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 194772992 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 195035136 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 195297280 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 195559424 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 195821568 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 196083712 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.71 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 196345856 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.42 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 196608000 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 196870144 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.00 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 197132288 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.16 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 197394432 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.84 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 197656576 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 197918720 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 198180864 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 198443008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 198705152 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.45 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 198967296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 199229440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.99 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 199491584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 199753728 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 200015872 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 200278016 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 200540160 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 200802304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.58 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 201064448 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.81 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 201326592 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.91 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 201588736 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.53 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 201850880 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 202113024 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.68 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 202375168 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.82 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 202637312 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 202899456 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 203161600 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.23 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 203423744 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 203685888 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 203948032 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 204210176 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.79 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 204472320 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.01 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 204734464 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 204996608 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.39 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 205258752 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 205520896 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 205783040 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.10 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 206045184 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 206307328 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 206569472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 206831616 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.34 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 207093760 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 207355904 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 45.08 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 207618048 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.41 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 207880192 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 46.16 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 208142336 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 208404480 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.93 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 208666624 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 208928768 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.48 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 209190912 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 209453056 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.42 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 209715200 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 209977344 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.84 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 210239488 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.69 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 210501632 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.57 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 210763776 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.42 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 211025920 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.84 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 211288064 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.57 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 211550208 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.19 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 211812352 sequences have been processed. [bwa_read_seq] 0.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 212074496 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 212336640 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.56 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 212598784 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 212860928 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 213123072 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.95 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 213385216 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.43 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 213647360 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 213909504 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.70 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 214171648 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 214433792 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.09 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 214695936 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 214958080 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.61 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 215220224 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.96 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 215482368 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.03 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 215744512 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 216006656 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 216268800 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.21 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 216530944 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 216793088 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 217055232 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.42 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 217317376 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 217579520 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.35 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 217841664 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.38 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218103808 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.61 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 218365952 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218628096 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.23 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 218890240 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.31 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 219152384 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.25 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 219414528 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 219676672 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.56 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 219938816 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.12 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 220200960 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.24 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 220463104 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 220725248 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.83 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 220987392 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 221249536 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.14 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 221511680 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.64 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 221773824 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 222035968 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.86 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 222298112 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.56 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 222560256 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 222822400 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.27 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 223084544 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.29 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 223346688 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 223608832 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.61 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 223870976 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.48 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 224133120 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.98 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 224395264 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.99 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 224657408 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 224919552 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.28 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 225181696 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.35 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 225443840 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.30 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 225705984 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.37 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 225968128 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.09 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 226230272 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 226492416 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.17 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 226754560 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 227016704 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.06 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 227278848 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.91 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 227540992 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.69 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 227803136 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.55 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 228065280 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.70 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 228327424 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 31.70 sec [bwa_aln_core] write to the disk... 0.08 sec [bwa_aln_core] 228589568 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 228851712 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.73 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 229113856 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.79 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 229376000 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.28 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 229638144 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.85 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 229900288 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 32.64 sec [bwa_aln_core] write to the disk... 0.09 sec [bwa_aln_core] 230162432 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.40 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 230424576 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.46 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 230686720 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.59 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 230948864 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.18 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 231211008 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.44 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 231473152 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 231735296 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.87 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 231997440 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 33.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 232259584 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.87 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 232521728 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.18 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 232783872 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 34.97 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 233046016 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 233308160 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.59 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 233570304 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 233832448 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 234094592 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.20 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 234356736 sequences have been processed. [bwa_read_seq] 0.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.98 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 234618880 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 234881024 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.54 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 235143168 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 36.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 235405312 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.47 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 235667456 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.02 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 235929600 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 236191744 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 39.18 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 236453888 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 38.62 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 236716032 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 37.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 236978176 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.87 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 237240320 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 237502464 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 237764608 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 238026752 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 35.24 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 238288896 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.72 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 238551040 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 238813184 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.63 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 239075328 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.95 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 239337472 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 239599616 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.74 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 239861760 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 240123904 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.85 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 240386048 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.63 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 240648192 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.95 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 240910336 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 241172480 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 241434624 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.54 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 241696768 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.74 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 241958912 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.00 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 242221056 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.47 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 242483200 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.17 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 242745344 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.61 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 243007488 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 44.78 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 243269632 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.11 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 243531776 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.27 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 243793920 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.58 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 244056064 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.37 sec [bwa_aln_core] write to the disk... 0.07 sec [bwa_aln_core] 244318208 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.55 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 244580352 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.75 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 244842496 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.29 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 245104640 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 245366784 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.34 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 245628928 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 245891072 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.39 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 246153216 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.33 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 246415360 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.75 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 246677504 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.96 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 246939648 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 247201792 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 247463936 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.44 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 247726080 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.02 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 247988224 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 248250368 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 248512512 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.75 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 248774656 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 40.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 249036800 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 249298944 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 43.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 249561088 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.41 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 249823232 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.15 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 250085376 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 41.77 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 250347520 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.40 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 250609664 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.55 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 250871808 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 42.61 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 251133952 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 251396096 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 251658240 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.46 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 251920384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 252182528 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 252444672 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 252706816 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 252968960 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 253231104 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 253493248 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.80 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 253755392 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.45 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 254017536 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 254279680 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.88 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 254541824 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 254803968 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.63 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 255066112 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.38 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 255328256 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 255590400 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 255852544 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.94 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 256114688 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.96 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 256376832 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 256638976 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.68 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 256901120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 257163264 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.22 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 257425408 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 257687552 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 257949696 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 258211840 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 258473984 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.77 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 258736128 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.75 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 258998272 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 259260416 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.50 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 259522560 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.80 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 259784704 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 260046848 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 260308992 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 260571136 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 260833280 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 261095424 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 261357568 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 261619712 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.66 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 261881856 sequences have been processed. [bwa_read_seq] 2.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262144000 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262406144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.26 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 262668288 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.58 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 262930432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.13 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 263192576 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.28 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 263454720 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.91 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 263716864 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 263979008 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.88 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 264241152 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 264503296 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 264765440 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.37 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 265027584 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 265289728 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 265551872 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 265814016 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.15 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 266076160 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.66 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 266338304 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 266600448 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 266862592 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 267124736 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.03 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 267386880 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 267649024 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.33 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 267911168 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 93.84 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 268173312 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 97.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 268435456 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 94.50 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 268697600 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.20 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 268959744 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 95.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 269221888 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 269484032 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 98.54 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 269746176 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 96.81 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 270008320 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 270270464 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.06 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 270532608 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.37 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 270794752 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.71 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 271056896 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 271319040 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 271581184 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 271843328 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.38 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 272105472 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 272367616 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 272629760 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.58 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 272891904 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.43 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 273154048 sequences have been processed. [bwa_read_seq] 3.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 273416192 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.15 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 273678336 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 273940480 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.14 sec [bwa_aln_core] write to the disk... 0.06 sec [bwa_aln_core] 274202624 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.12 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 274464768 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.57 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 274726912 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 274989056 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 275251200 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.98 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 275513344 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.98 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 275775488 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.41 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 276037632 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.05 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 276299776 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.76 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 276561920 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 276824064 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 277086208 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.53 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 277348352 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... 0.04 sec [bwa_aln_core] 277610496 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.34 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 277872640 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 278134784 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.90 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 278396928 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.79 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 278659072 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.98 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 278921216 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.27 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 279183360 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 78.53 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 279445504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.73 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 279707648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.52 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 279969792 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 280231936 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.60 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 280494080 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.00 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 280756224 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 281018368 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 281280512 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 281542656 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.04 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 281804800 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... 0.04 sec [bwa_aln_core] 282066944 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 282329088 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.42 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 282591232 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.62 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 282853376 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.21 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 283115520 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 283377664 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.51 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 283639808 sequences have been processed. [bwa_read_seq] 2.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.06 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 283901952 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 284164096 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 284426240 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.48 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 284688384 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.89 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 284950528 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 285212672 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.04 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 285474816 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 285736960 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.29 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 285999104 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 286261248 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.70 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 286523392 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.76 sec [bwa_aln_core] write to the disk... 0.02 sec [bwa_aln_core] 286785536 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 287047680 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 287309824 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 287571968 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.45 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 287834112 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.73 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 288096256 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.13 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 288358400 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 60.92 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 288620544 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 59.10 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 288882688 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.16 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 289144832 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.30 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 289406976 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 289669120 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.93 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 289931264 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 61.64 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 290193408 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.72 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 290455552 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.85 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 290717696 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.86 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 290979840 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.32 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 291241984 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.31 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 291504128 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.33 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 291766272 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 292028416 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.08 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 292290560 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 292552704 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.35 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 292814848 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.76 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 293076992 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.23 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 293339136 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.80 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 293601280 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 293863424 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 294125568 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.30 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 294387712 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.78 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 294649856 sequences have been processed. [bwa_read_seq] 0.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 62.93 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 294912000 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 68.70 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 295174144 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.95 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 295436288 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.49 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 295698432 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 65.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 295960576 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 67.64 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 296222720 sequences have been processed. [bwa_read_seq] 4.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.14 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 296484864 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 64.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 296747008 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 297009152 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.65 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 297271296 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.65 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 297533440 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 297795584 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.64 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 298057728 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.53 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 298319872 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 298582016 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.52 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 298844160 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.20 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 299106304 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 299368448 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.64 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 299630592 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.27 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 299892736 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.86 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 300154880 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.83 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 300417024 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 300679168 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 300941312 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.19 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 301203456 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 301465600 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.02 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 301727744 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.26 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 301989888 sequences have been processed. [bwa_read_seq] 0.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 302252032 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 77.49 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 302514176 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.31 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 302776320 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.03 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 303038464 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.25 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 303300608 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 91.46 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 303562752 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.87 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 303824896 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.51 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 304087040 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.49 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 304349184 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.75 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 304611328 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 304873472 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 80.67 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 305135616 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.82 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 305397760 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.07 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 305659904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.90 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 305922048 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 306184192 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 306446336 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 81.20 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 306708480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 306970624 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.93 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 307232768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.55 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 307494912 sequences have been processed. [bwa_read_seq] 0.9% 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] 307757056 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.04 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 308019200 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 308281344 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 66.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 308543488 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 79.36 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 308805632 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.00 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 309067776 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.40 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 309329920 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.47 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 309592064 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.18 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 309854208 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.81 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 310116352 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.42 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 310378496 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 310640640 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.40 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 310902784 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.91 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 311164928 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.12 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 311427072 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.47 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 311689216 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 82.48 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 311951360 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 312213504 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.97 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 312475648 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 69.19 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 312737792 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 312999936 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 71.72 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 313262080 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 73.60 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 313524224 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 313786368 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 72.59 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 314048512 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 63.29 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 314310656 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.97 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 314572800 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 86.74 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 314834944 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.70 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 315097088 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.69 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 315359232 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.99 sec [bwa_aln_core] write to the disk... 0.05 sec [bwa_aln_core] 315621376 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 85.02 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 315883520 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 90.32 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 316145664 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 89.89 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 316407808 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.76 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 316669952 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.54 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 316932096 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.68 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 317194240 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 87.20 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 317456384 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.96 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 317718528 sequences have been processed. [bwa_read_seq] 1.0% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 84.57 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 317980672 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 318242816 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 318504960 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 75.66 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 318767104 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.28 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 319029248 sequences have been processed. [bwa_read_seq] 0.8% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 74.84 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 319291392 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 76.67 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 319553536 sequences have been processed. [bwa_read_seq] 0.9% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 83.95 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 319815680 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 92.18 sec [bwa_aln_core] write to the disk... 0.04 sec [bwa_aln_core] 320077824 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] calculate SA coordinate... 88.74 sec [bwa_aln_core] write to the disk... 0.03 sec [bwa_aln_core] 320304843 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/R339W_allReps.fastq.gz [main] Real time: 15096.407 sec; CPU: 56549.120 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/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam
# SYS command. line 149
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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-------------------- 46786 (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] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 97.84 sec [bwa_aln_core] refine gapped alignments... 14.09 sec [bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences. 0.75 sec [bwa_aln_core] 262144 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.46 sec [bwa_aln_core] refine gapped alignments... 14.93 sec [bwa_aln_core] print alignments... 1.01 sec [bwa_aln_core] 524288 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 93.02 sec [bwa_aln_core] refine gapped alignments... 6.83 sec [bwa_aln_core] print alignments... 0.72 sec [bwa_aln_core] 786432 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 37.00 sec [bwa_aln_core] refine gapped alignments... 7.68 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 1048576 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.18 sec [bwa_aln_core] refine gapped alignments... 10.68 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 1310720 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 90.30 sec [bwa_aln_core] refine gapped alignments... 15.04 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 1572864 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.15 sec [bwa_aln_core] refine gapped alignments... 6.91 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 1835008 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.91 sec [bwa_aln_core] refine gapped alignments... 14.27 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 2097152 sequences have been processed. [bwa_read_seq] 2.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.44 sec [bwa_aln_core] refine gapped alignments... 3.02 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 2359296 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 96.93 sec [bwa_aln_core] refine gapped alignments... 10.33 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 2621440 sequences have been processed. [bwa_read_seq] 10.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.44 sec [bwa_aln_core] refine gapped alignments... 15.93 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 2883584 sequences have been processed. [bwa_read_seq] 12.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 83.35 sec [bwa_aln_core] refine gapped alignments... 3.99 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 3145728 sequences have been processed. [bwa_read_seq] 12.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 41.76 sec [bwa_aln_core] refine gapped alignments... 4.21 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 3407872 sequences have been processed. [bwa_read_seq] 11.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 25.24 sec [bwa_aln_core] refine gapped alignments... 16.35 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 3670016 sequences have been processed. [bwa_read_seq] 9.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 43.49 sec [bwa_aln_core] refine gapped alignments... 13.25 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 3932160 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 52.18 sec [bwa_aln_core] refine gapped alignments... 14.13 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 4194304 sequences have been processed. [bwa_read_seq] 4.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 52.58 sec [bwa_aln_core] refine gapped alignments... 11.24 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 4456448 sequences have been processed. [bwa_read_seq] 3.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.87 sec [bwa_aln_core] refine gapped alignments... 9.30 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 4718592 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 52.77 sec [bwa_aln_core] refine gapped alignments... 2.80 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 4980736 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.46 sec [bwa_aln_core] refine gapped alignments... 4.80 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 5242880 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.74 sec [bwa_aln_core] refine gapped alignments... 2.79 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 5505024 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.40 sec [bwa_aln_core] refine gapped alignments... 5.33 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 5767168 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.00 sec [bwa_aln_core] refine gapped alignments... 6.80 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 6029312 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.35 sec [bwa_aln_core] refine gapped alignments... 0.38 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 6291456 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.92 sec [bwa_aln_core] refine gapped alignments... 5.19 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 6553600 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 9.85 sec [bwa_aln_core] refine gapped alignments... 2.27 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 6815744 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 19.07 sec [bwa_aln_core] refine gapped alignments... 9.17 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 7077888 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.27 sec [bwa_aln_core] refine gapped alignments... 12.55 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 7340032 sequences have been processed. [bwa_read_seq] 2.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.25 sec [bwa_aln_core] refine gapped alignments... 9.14 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 7602176 sequences have been processed. [bwa_read_seq] 6.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 58.25 sec [bwa_aln_core] refine gapped alignments... 5.93 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 7864320 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.44 sec [bwa_aln_core] refine gapped alignments... 15.19 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 8126464 sequences have been processed. [bwa_read_seq] 13.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.36 sec [bwa_aln_core] refine gapped alignments... 2.33 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 8388608 sequences have been processed. [bwa_read_seq] 13.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.96 sec [bwa_aln_core] refine gapped alignments... 6.95 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 8650752 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.91 sec [bwa_aln_core] refine gapped alignments... 5.54 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 8912896 sequences have been processed. [bwa_read_seq] 11.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.16 sec [bwa_aln_core] refine gapped alignments... 9.48 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 9175040 sequences have been processed. [bwa_read_seq] 9.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 79.01 sec [bwa_aln_core] refine gapped alignments... 9.53 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 9437184 sequences have been processed. [bwa_read_seq] 6.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.77 sec [bwa_aln_core] refine gapped alignments... 12.31 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 9699328 sequences have been processed. [bwa_read_seq] 5.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.99 sec [bwa_aln_core] refine gapped alignments... 3.79 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 9961472 sequences have been processed. [bwa_read_seq] 3.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.27 sec [bwa_aln_core] refine gapped alignments... 10.45 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 10223616 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.41 sec [bwa_aln_core] refine gapped alignments... 10.49 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 10485760 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.57 sec [bwa_aln_core] refine gapped alignments... 13.90 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 10747904 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.99 sec [bwa_aln_core] refine gapped alignments... 6.28 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 11010048 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 29.36 sec [bwa_aln_core] refine gapped alignments... 1.88 sec [bwa_aln_core] print alignments... 0.49 sec [bwa_aln_core] 11272192 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.53 sec [bwa_aln_core] refine gapped alignments... 14.38 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 11534336 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 50.68 sec [bwa_aln_core] refine gapped alignments... 4.51 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 11796480 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.78 sec [bwa_aln_core] refine gapped alignments... 6.55 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 12058624 sequences have been processed. [bwa_read_seq] 1.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 26.20 sec [bwa_aln_core] refine gapped alignments... 1.26 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 12320768 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.96 sec [bwa_aln_core] refine gapped alignments... 0.47 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 12582912 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.88 sec [bwa_aln_core] refine gapped alignments... 4.59 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 12845056 sequences have been processed. [bwa_read_seq] 4.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.11 sec [bwa_aln_core] refine gapped alignments... 0.51 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 13107200 sequences have been processed. [bwa_read_seq] 8.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.42 sec [bwa_aln_core] refine gapped alignments... 3.17 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 13369344 sequences have been processed. [bwa_read_seq] 11.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.38 sec [bwa_aln_core] refine gapped alignments... 5.60 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 13631488 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 47.29 sec [bwa_aln_core] refine gapped alignments... 5.88 sec [bwa_aln_core] print alignments... 0.67 sec [bwa_aln_core] 13893632 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 45.97 sec [bwa_aln_core] refine gapped alignments... 10.59 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 14155776 sequences have been processed. [bwa_read_seq] 10.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.02 sec [bwa_aln_core] refine gapped alignments... 10.31 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 14417920 sequences have been processed. [bwa_read_seq] 8.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 82.63 sec [bwa_aln_core] refine gapped alignments... 13.48 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 14680064 sequences have been processed. [bwa_read_seq] 6.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 69.17 sec [bwa_aln_core] refine gapped alignments... 12.76 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 14942208 sequences have been processed. [bwa_read_seq] 4.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.71 sec [bwa_aln_core] refine gapped alignments... 8.34 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 15204352 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.87 sec [bwa_aln_core] refine gapped alignments... 12.89 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 15466496 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 64.47 sec [bwa_aln_core] refine gapped alignments... 18.63 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 15728640 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.86 sec [bwa_aln_core] refine gapped alignments... 16.07 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 15990784 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.77 sec [bwa_aln_core] refine gapped alignments... 10.65 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 16252928 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 63.93 sec [bwa_aln_core] refine gapped alignments... 6.52 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 16515072 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 67.15 sec [bwa_aln_core] refine gapped alignments... 3.60 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 16777216 sequences have been processed. [bwa_read_seq] 1.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 24.90 sec [bwa_aln_core] refine gapped alignments... 6.12 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 17039360 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.45 sec [bwa_aln_core] refine gapped alignments... 9.21 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 17301504 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 62.49 sec [bwa_aln_core] refine gapped alignments... 15.82 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 17563648 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 65.28 sec [bwa_aln_core] refine gapped alignments... 13.14 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 17825792 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.07 sec [bwa_aln_core] refine gapped alignments... 15.08 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 18087936 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.50 sec [bwa_aln_core] refine gapped alignments... 16.39 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 18350080 sequences have been processed. [bwa_read_seq] 4.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.77 sec [bwa_aln_core] refine gapped alignments... 19.86 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 18612224 sequences have been processed. [bwa_read_seq] 9.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.35 sec [bwa_aln_core] refine gapped alignments... 17.68 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 18874368 sequences have been processed. [bwa_read_seq] 12.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 83.36 sec [bwa_aln_core] refine gapped alignments... 16.13 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 19136512 sequences have been processed. [bwa_read_seq] 12.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 69.33 sec [bwa_aln_core] refine gapped alignments... 15.59 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 19398656 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 81.51 sec [bwa_aln_core] refine gapped alignments... 8.23 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 19660800 sequences have been processed. [bwa_read_seq] 9.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 89.28 sec [bwa_aln_core] refine gapped alignments... 10.45 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 19922944 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 85.27 sec [bwa_aln_core] refine gapped alignments... 8.67 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 20185088 sequences have been processed. [bwa_read_seq] 5.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 73.85 sec [bwa_aln_core] refine gapped alignments... 14.09 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 20447232 sequences have been processed. [bwa_read_seq] 3.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 81.32 sec [bwa_aln_core] refine gapped alignments... 13.05 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 20709376 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.79 sec [bwa_aln_core] refine gapped alignments... 13.10 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 20971520 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.53 sec [bwa_aln_core] refine gapped alignments... 11.73 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 21233664 sequences have been processed. [bwa_read_seq] 1.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.02 sec [bwa_aln_core] refine gapped alignments... 15.38 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 21495808 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.76 sec [bwa_aln_core] refine gapped alignments... 11.71 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 21757952 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.11 sec [bwa_aln_core] refine gapped alignments... 13.74 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 22020096 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.59 sec [bwa_aln_core] refine gapped alignments... 13.23 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 22282240 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.63 sec [bwa_aln_core] refine gapped alignments... 11.47 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 22544384 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.07 sec [bwa_aln_core] refine gapped alignments... 12.19 sec [bwa_aln_core] print alignments... 0.52 sec [bwa_aln_core] 22806528 sequences have been processed. [bwa_read_seq] 1.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 78.14 sec [bwa_aln_core] refine gapped alignments... 11.55 sec [bwa_aln_core] print alignments... 0.56 sec [bwa_aln_core] 23068672 sequences have been processed. [bwa_read_seq] 1.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 84.11 sec [bwa_aln_core] refine gapped alignments... 11.08 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 23330816 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 66.77 sec [bwa_aln_core] refine gapped alignments... 13.57 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 23592960 sequences have been processed. [bwa_read_seq] 6.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 94.87 sec [bwa_aln_core] refine gapped alignments... 3.40 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 23855104 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 71.44 sec [bwa_aln_core] refine gapped alignments... 6.74 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 24117248 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.87 sec [bwa_aln_core] refine gapped alignments... 4.32 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 24379392 sequences have been processed. [bwa_read_seq] 14.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 82.66 sec [bwa_aln_core] refine gapped alignments... 3.33 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 24641536 sequences have been processed. [bwa_read_seq] 13.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 88.47 sec [bwa_aln_core] refine gapped alignments... 7.99 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 24903680 sequences have been processed. [bwa_read_seq] 11.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 76.56 sec [bwa_aln_core] refine gapped alignments... 4.24 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 25165824 sequences have been processed. [bwa_read_seq] 9.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.96 sec [bwa_aln_core] refine gapped alignments... 13.69 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 25427968 sequences have been processed. [bwa_read_seq] 7.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 80.53 sec [bwa_aln_core] refine gapped alignments... 16.17 sec [bwa_aln_core] print alignments... 0.62 sec [bwa_aln_core] 25690112 sequences have been processed. [bwa_read_seq] 5.5% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 88.51 sec [bwa_aln_core] refine gapped alignments... 14.98 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 25952256 sequences have been processed. [bwa_read_seq] 3.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 70.55 sec [bwa_aln_core] refine gapped alignments... 7.15 sec [bwa_aln_core] print alignments... 0.63 sec [bwa_aln_core] 26214400 sequences have been processed. [bwa_read_seq] 2.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 72.00 sec [bwa_aln_core] refine gapped alignments... 12.64 sec [bwa_aln_core] print alignments... 0.54 sec [bwa_aln_core] 26476544 sequences have been processed. [bwa_read_seq] 2.1% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 74.32 sec [bwa_aln_core] refine gapped alignments... 13.75 sec [bwa_aln_core] print alignments... 0.60 sec [bwa_aln_core] 26738688 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 77.90 sec [bwa_aln_core] refine gapped alignments... 9.69 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 27000832 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 79.34 sec [bwa_aln_core] refine gapped alignments... 10.21 sec [bwa_aln_core] print alignments... 0.51 sec [bwa_aln_core] 27262976 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 73.58 sec [bwa_aln_core] refine gapped alignments... 10.65 sec [bwa_aln_core] print alignments... 0.53 sec [bwa_aln_core] 27525120 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.03 sec [bwa_aln_core] refine gapped alignments... 9.28 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 27787264 sequences have been processed. [bwa_read_seq] 1.3% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 54.07 sec [bwa_aln_core] refine gapped alignments... 11.95 sec [bwa_aln_core] print alignments... 0.48 sec [bwa_aln_core] 28049408 sequences have been processed. [bwa_read_seq] 1.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.65 sec [bwa_aln_core] refine gapped alignments... 4.99 sec [bwa_aln_core] print alignments... 0.47 sec [bwa_aln_core] 28311552 sequences have been processed. [bwa_read_seq] 1.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 49.41 sec [bwa_aln_core] refine gapped alignments... 0.53 sec [bwa_aln_core] print alignments... 0.50 sec [bwa_aln_core] 28573696 sequences have been processed. [bwa_read_seq] 2.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 50.82 sec [bwa_aln_core] refine gapped alignments... 0.39 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 28835840 sequences have been processed. [bwa_read_seq] 5.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.95 sec [bwa_aln_core] refine gapped alignments... 1.13 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 29097984 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 57.37 sec [bwa_aln_core] refine gapped alignments... 8.89 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 29360128 sequences have been processed. [bwa_read_seq] 12.2% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 55.66 sec [bwa_aln_core] refine gapped alignments... 4.74 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 29622272 sequences have been processed. [bwa_read_seq] 12.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 61.78 sec [bwa_aln_core] refine gapped alignments... 7.88 sec [bwa_aln_core] print alignments... 0.68 sec [bwa_aln_core] 29884416 sequences have been processed. [bwa_read_seq] 11.6% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 30.07 sec [bwa_aln_core] refine gapped alignments... 2.03 sec [bwa_aln_core] print alignments... 0.61 sec [bwa_aln_core] 30146560 sequences have been processed. [bwa_read_seq] 9.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 46.31 sec [bwa_aln_core] refine gapped alignments... 5.81 sec [bwa_aln_core] print alignments... 0.59 sec [bwa_aln_core] 30408704 sequences have been processed. [bwa_read_seq] 7.7% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 50.94 sec [bwa_aln_core] refine gapped alignments... 9.52 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 30670848 sequences have been processed. [bwa_read_seq] 5.8% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 56.93 sec [bwa_aln_core] refine gapped alignments... 7.33 sec [bwa_aln_core] print alignments... 0.57 sec [bwa_aln_core] 30932992 sequences have been processed. [bwa_read_seq] 4.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 75.05 sec [bwa_aln_core] refine gapped alignments... 9.44 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 31195136 sequences have been processed. [bwa_read_seq] 3.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 68.45 sec [bwa_aln_core] refine gapped alignments... 10.38 sec [bwa_aln_core] print alignments... 0.55 sec [bwa_aln_core] 31457280 sequences have been processed. [bwa_read_seq] 2.4% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 60.08 sec [bwa_aln_core] refine gapped alignments... 2.86 sec [bwa_aln_core] print alignments... 0.58 sec [bwa_aln_core] 31719424 sequences have been processed. [bwa_read_seq] 1.9% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 73.15 sec [bwa_aln_core] refine gapped alignments... 4.56 sec [bwa_aln_core] print alignments... 0.64 sec [bwa_aln_core] 31981568 sequences have been processed. [bwa_read_seq] 2.0% bases are trimmed. [bwa_aln_core] convert to sequence coordinate... 78.25 sec [bwa_aln_core] refine gapped alignments... 8.63 sec [bwa_aln_core] print alignments... 0.10 sec [bwa_aln_core] 32022635 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/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.fastq.gz [main] Real time: 9597.471 sec; CPU: 9342.881 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/R339W/out/align/rep1/R339W_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/R339W_allReps.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.bam
# SYS command. line 149
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/rep1/R339W_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--------------------
39260 (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] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 57.38 sec
[bwa_aln_core] refine gapped alignments... 5.19 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 96 sequences.
0.72 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.72 sec
[bwa_aln_core] refine gapped alignments... 8.18 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.36 sec
[bwa_aln_core] refine gapped alignments... 3.73 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 24.47 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 38.98 sec
[bwa_aln_core] refine gapped alignments... 7.62 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 47.42 sec
[bwa_aln_core] refine gapped alignments... 8.28 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 55.61 sec
[bwa_aln_core] refine gapped alignments... 7.35 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 63.53 sec
[bwa_aln_core] refine gapped alignments... 13.66 sec
[bwa_aln_core] print alignments... 0.71 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 67.14 sec
[bwa_aln_core] refine gapped alignments... 12.31 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.86 sec
[bwa_aln_core] refine gapped alignments... 4.32 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.55 sec
[bwa_aln_core] refine gapped alignments... 7.22 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 84.41 sec
[bwa_aln_core] refine gapped alignments... 10.30 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 86.36 sec
[bwa_aln_core] refine gapped alignments... 10.56 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 76.05 sec
[bwa_aln_core] refine gapped alignments... 3.88 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.23 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.27 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 46.02 sec
[bwa_aln_core] refine gapped alignments... 0.40 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 44.10 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.05 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 53.78 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 49.62 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.99 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.44 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 48.49 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 54.52 sec
[bwa_aln_core] refine gapped alignments... 2.10 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 74.15 sec
[bwa_aln_core] refine gapped alignments... 5.81 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 82.80 sec
[bwa_aln_core] refine gapped alignments... 7.50 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 66.77 sec
[bwa_aln_core] refine gapped alignments... 6.23 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.81 sec
[bwa_aln_core] refine gapped alignments... 6.55 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 71.72 sec
[bwa_aln_core] refine gapped alignments... 7.35 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 43.15 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.54 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.33 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.17 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.55 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.46 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.78 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.32 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.76 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.62 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.62 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.62 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.77 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.31 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.06 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.35 sec
[bwa_aln_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.12 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.97 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.73 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.22 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.07 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.80 sec
[bwa_aln_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.77 sec
[bwa_aln_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.99 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.58 sec
[bwa_aln_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.95 sec
[bwa_aln_core] refine gapped alignments... 0.43 sec
[bwa_aln_core] print alignments... 0.76 sec
[bwa_aln_core] 26476544 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.80 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 26738688 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 27000832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 27262976 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 27525120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 27787264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 28049408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 28311552 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 28573696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.41 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 28835840 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 29097984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 29360128 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 29622272 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 29884416 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 30146560 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 30408704 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.81 sec
[bwa_aln_core] 30670848 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 30932992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 31195136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 31457280 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.94 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 31719424 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 31981568 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.82 sec
[bwa_aln_core] 32243712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 32505856 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 32768000 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.60 sec
[bwa_aln_core] 33030144 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 33292288 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 33554432 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 33816576 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 34078720 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 34340864 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 34603008 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 34865152 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 35127296 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 35389440 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 35651584 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 35913728 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 36175872 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 36438016 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.52 sec
[bwa_aln_core] 36700160 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 36962304 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 37224448 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 37486592 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 37748736 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 38010880 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 38273024 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 38535168 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.35 sec
[bwa_aln_core] 38797312 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.42 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 39059456 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 39321600 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 39583744 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 39845888 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.79 sec
[bwa_aln_core] 40108032 sequences have been processed.
[bwa_read_seq] 1.2% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.82 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 40370176 sequences have been processed.
[bwa_read_seq] 1.0% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 40632320 sequences have been processed.
[bwa_read_seq] 0.9% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 40894464 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 41156608 sequences have been processed.
[bwa_read_seq] 0.8% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 41418752 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.74 sec
[bwa_aln_core] 41680896 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 41943040 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 42205184 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 42467328 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 42729472 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 42991616 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 43253760 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 43515904 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.55 sec
[bwa_aln_core] 43778048 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 44040192 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.65 sec
[bwa_aln_core] 44302336 sequences have been processed.
[bwa_read_seq] 0.4% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 44564480 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 44826624 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 45088768 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 45350912 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 45613056 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 45875200 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 46137344 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.64 sec
[bwa_aln_core] 46399488 sequences have been processed.
[bwa_read_seq] 0.6% 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... 0.64 sec
[bwa_aln_core] 46661632 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.59 sec
[bwa_aln_core] 46923776 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.67 sec
[bwa_aln_core] 47185920 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 47448064 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.53 sec
[bwa_aln_core] 47710208 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.75 sec
[bwa_aln_core] 47972352 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 48234496 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 48496640 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 48758784 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.48 sec
[bwa_aln_core] 49020928 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.44 sec
[bwa_aln_core] 49283072 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 49545216 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 49807360 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 50069504 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 50331648 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.83 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 50593792 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 50855936 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.23 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 51118080 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 51380224 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 51642368 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 51904512 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 52166656 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 52428800 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.51 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 52690944 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.28 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 52953088 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 53215232 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 53477376 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.27 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 53739520 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 54001664 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 54263808 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.30 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 54525952 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.29 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 54788096 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.25 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.69 sec
[bwa_aln_core] 55050240 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.24 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 55312384 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 3.16 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 55574528 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 55836672 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 56098816 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 56360960 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 56623104 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.61 sec
[bwa_aln_core] 56885248 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 57147392 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.59 sec
[bwa_aln_core] 57409536 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.54 sec
[bwa_aln_core] 57671680 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.57 sec
[bwa_aln_core] 57933824 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.91 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.46 sec
[bwa_aln_core] 58195968 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.34 sec
[bwa_aln_core] 58458112 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.37 sec
[bwa_aln_core] 58720256 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.50 sec
[bwa_aln_core] 58982400 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.47 sec
[bwa_aln_core] 59244544 sequences have been processed.
[bwa_read_seq] 0.5% 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... 0.50 sec
[bwa_aln_core] 59506688 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.62 sec
[bwa_aln_core] 59768832 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.81 sec
[bwa_aln_core] refine gapped alignments... 0.37 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 60030976 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.64 sec
[bwa_aln_core] 60293120 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.43 sec
[bwa_aln_core] 60555264 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 60817408 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.78 sec
[bwa_aln_core] 61079552 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.72 sec
[bwa_aln_core] 61341696 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.49 sec
[bwa_aln_core] 61603840 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 61865984 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.56 sec
[bwa_aln_core] 62128128 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.88 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.41 sec
[bwa_aln_core] 62390272 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.48 sec
[bwa_aln_core] 62652416 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.85 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.63 sec
[bwa_aln_core] 62914560 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.42 sec
[bwa_aln_core] 63176704 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.36 sec
[bwa_aln_core] 63438848 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 63700992 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.84 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.45 sec
[bwa_aln_core] 63963136 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.92 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.68 sec
[bwa_aln_core] 64225280 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.86 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.39 sec
[bwa_aln_core] 64487424 sequences have been processed.
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.93 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.66 sec
[bwa_aln_core] 64749568 sequences have been processed.
[bwa_read_seq] 0.7% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.89 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.60 sec
[bwa_aln_core] 65011712 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.90 sec
[bwa_aln_core] refine gapped alignments... 0.38 sec
[bwa_aln_core] print alignments... 0.51 sec
[bwa_aln_core] 65273856 sequences have been processed.
[bwa_read_seq] 0.6% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... 2.87 sec
[bwa_aln_core] refine gapped alignments... 0.39 sec
[bwa_aln_core] print alignments... sambamba-sort: Unable to write to stream
--------------------Post mortem info--------------------
==============================================================
job_number: 9892
submission_time: Thu Sep 29 19:54:37 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_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
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/chipseq.bds.20160929_154250_022_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/chipseq.bds.20160929_154250_022_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_13.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 58475 22,USER=imk1,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/38,LOGNAME=imk1,_=/usr/bin/bds,XDG_SESSION_ID=418,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/keras,SGE_ROOT=/var/lib/gridengine,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,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,SGE_CELL=default,DISPLAY=localhost:19.0,STY=40099.R339W.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_eHVWt0,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 58475 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/software/python_anaconda/2.2.0/bin/python:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
parallel environment: shm range: 4
scheduling info: queue instance "q@mitra" dropped because it is temporarily not available
queue instance "q@amold" dropped because it is full
queue instance "q@wotan" dropped because it is full
queue instance "amd.q@surya" dropped because it is full
queue instance "amd.q@kadru" dropped because it is full
queue instance "amd.q@nandi" dropped because it is full
queue instance "amd.q@kali" dropped because it is full
| ||||||||||||||||||||||||||||||||||||||||
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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/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam -n -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
samtools view -h /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam; \
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.qnmsrt.bam; \
else \
samtools view -F 1804 -q 30 -u /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.bam | \
sambamba sort -t 1 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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-------------------- 5985 (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 ${MARKDUP} \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
picard MarkDuplicates \
INPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam" OUTPUT="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam" \
METRICS_FILE="/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 380
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 45887 (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 20:29:25 PDT 2016] net.sf.picard.sam.MarkDuplicates INPUT=[/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.filt.bam] OUTPUT=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam METRICS_FILE=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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 20:29:25 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 2016-09-29 20:29:25 MarkDuplicates Start of doWork freeMemory: 255389840; totalMemory: 257294336; maxMemory: 3817799680 INFO 2016-09-29 20:29:25 MarkDuplicates Reading input file and constructing read end information. INFO 2016-09-29 20:29:25 MarkDuplicates Will retain up to 15149998 data points before spilling to disk. INFO 2016-09-29 20:29:29 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:169,651,309 INFO 2016-09-29 20:29:29 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:32 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr2:120,600,340 INFO 2016-09-29 20:29:32 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:35 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr3:96,659,413 INFO 2016-09-29 20:29:35 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:39 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr4:108,195,091 INFO 2016-09-29 20:29:39 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:42 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr5:103,594,339 INFO 2016-09-29 20:29:42 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:46 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr6:98,592,333 INFO 2016-09-29 20:29:46 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:49 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr7:114,109,505 INFO 2016-09-29 20:29:49 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:54 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 4s. Last read position: chr8:121,515,352 INFO 2016-09-29 20:29:54 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:29:59 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 4s. Last read position: chr10:14,536,964 INFO 2016-09-29 20:29:59 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:02 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr11:32,924,585 INFO 2016-09-29 20:30:02 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:06 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 4s. Last read position: chr12:41,050,039 INFO 2016-09-29 20:30:06 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:09 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr13:80,878,598 INFO 2016-09-29 20:30:09 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:13 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: chr15:12,027,335 INFO 2016-09-29 20:30:13 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:16 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: chr16:56,024,589 INFO 2016-09-29 20:30:16 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:19 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: chr18:10,030,498 INFO 2016-09-29 20:30:19 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:28 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 9s. Last read position: chrX:36,565,109 INFO 2016-09-29 20:30:28 MarkDuplicates Tracking 0 as yet unmatched pairs. 0 records in RAM. INFO 2016-09-29 20:30:29 MarkDuplicates Read 16572675 records. 0 pairs never matched. INFO 2016-09-29 20:30:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 2059836552; totalMemory: 2137718784; maxMemory: 3817799680 INFO 2016-09-29 20:30:30 MarkDuplicates Will retain up to 119306240 duplicate indices before spilling to disk. INFO 2016-09-29 20:30:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2016-09-29 20:30:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2016-09-29 20:30:35 MarkDuplicates Sorting list of duplicate records. INFO 2016-09-29 20:30:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 1432935712; totalMemory: 2405040128; maxMemory: 3817799680 INFO 2016-09-29 20:30:36 MarkDuplicates Marking 13188493 records as duplicates. INFO 2016-09-29 20:30:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2016-09-29 20:32:36 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 120s. Last read position: chr11:32,924,585 INFO 2016-09-29 20:33:56 MarkDuplicates Before output close freeMemory: 2233338232; totalMemory: 2253324288; maxMemory: 3817799680 INFO 2016-09-29 20:33:56 MarkDuplicates After output close freeMemory: 2197947952; totalMemory: 2217934848; maxMemory: 3817799680 [Thu Sep 29 20:33:56 PDT 2016] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 4.53 minutes. Runtime.totalMemory()=2217934848 | ||||||||||||||||||||||||||||||||||||||||
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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/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.dupmark.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
# SYS command. line 153
sambamba index -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam
# SYS command. line 155
sambamba flagstat -t 1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.flagstat.qc
# SYS command. line 165
bedtools bamtobed -i /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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/R339W/out/qc/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.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-------------------- 6826 (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/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.bam | awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}' | gzip -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/ctl1/r120621A_l1i7_aB180__wt__bioBirAonly.nodup.tagAlign.gz
# SYS command. line 511
echo
# SYS command. line 513
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout-------------------- 7127 (process ID) old priority 0, new priority 10 Waiting for 52 seconds. --------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH |
| Type | Name | Value |
|---|---|---|
| string | _ | /usr/bin/bds |
| bool | allowEmpty | false |
| string[] | args | [-title, R339W, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out, -fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/R339W_allReps.fastq.gz, -ctl_fastq, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/r120621A_l1i7_aB180__wt__bioBirAonly.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/R339W |
| 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/R339W |
| 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 | 40099.R339W.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 |