Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr |
Num | 1 | ID | task.align_etc.trim_adapters_PE_rep1.line_57.id_6 | Name | trim_adapters_PE rep1 | Thread | thread_20 | PID | 29438 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-12 21:14:12 | End | 2016-05-12 23:30:46 | Elapsed | 02:16:33 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz
| Dependencies | | |
# SYS command. line 59
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 61
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1
# SYS command. line 62
$(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC7/ATAC7-trimmed-pair2.fastq.gz
# SYS command. line 63
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq
# SYS command. line 64
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq
--------------------Stdout--------------------
ATAC7-trimmed-pair1.trim.fastq
ATAC7-trimmed-pair2.trim.fastq
--------------------Stderr--------------------
95851404 sequences total
47972459 sequences trimmed with 0 mismatches
3950183 sequences trimmed with 1 mismatch
23 mean number of bases trimmed for reads requiring trimming
|
Num | 2 | ID | task.align_etc.trim_adapters_PE_rep2.line_57.id_7 | Name | trim_adapters_PE rep2 | Thread | thread_21 | PID | 29444 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-12 21:14:13 | End | 2016-05-12 23:01:11 | Elapsed | 01:46:58 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair2.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz
| Dependencies | | |
# SYS command. line 59
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 61
cd /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2
# SYS command. line 62
$(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC8/ATAC8-trimmed-pair2.fastq.gz
# SYS command. line 63
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq
# SYS command. line 64
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq
--------------------Stdout--------------------
ATAC8-trimmed-pair1.trim.fastq
ATAC8-trimmed-pair2.trim.fastq
--------------------Stderr--------------------
73645821 sequences total
36406945 sequences trimmed with 0 mismatches
3136472 sequences trimmed with 1 mismatch
22 mean number of bases trimmed for reads requiring trimming
|
Num | 3 | ID | task.align_bowtie2.bowtie2_PE_rep2.line_133.id_8 | Name | bowtie2_PE rep2 | Thread | thread_21 | PID | 47486 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 2 | Mem | | | Start | 2016-05-12 23:01:12 | End | 2016-05-12 23:01:12 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.align.log
| Dependencies | | |
# SYS command. line 135
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 139
bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE
# SYS command. line 142
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam
|
Num | 4 | ID | task.postalign_bam.dedup_bam_PE_rep2.line_215.id_9 | Name | dedup_bam_PE rep2 | Thread | thread_21 | PID | 47501 | | OK | false | Exit Code | 1 | Retries | | State | ERROR | Dep. | ERROR | Cpus | 1 | Mem | | | Start | 2016-05-12 23:01:13 | End | 2016-05-12 23:01:13 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
| Dependencies | | |
# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
echo
# SYS command. line 229
samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark
# SYS command. line 230
echo
# SYS command. line 237
samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 243
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 244
export MAX_JAVA_MEM="12G"
# SYS command. line 247
if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
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{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/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep2/ATAC8-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep2/ATAC8-trimmed-pair1.trim.PE2SE.dupmark.bam
--------------------Stdout--------------------
--------------------Stderr--------------------
Error: Unable to access jarfile /picard.jar
|
Num | 5 | ID | task.align_bowtie2.bowtie2_PE_rep1.line_133.id_10 | Name | bowtie2_PE rep1 | Thread | thread_20 | PID | 50261 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 2 | Mem | | | Start | 2016-05-12 23:30:47 | End | 2016-05-12 23:30:47 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.align.log
| Dependencies | | |
# SYS command. line 135
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 139
bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
-1 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE
# SYS command. line 142
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam
|
Num | 6 | ID | task.postalign_bam.dedup_bam_PE_rep1.line_215.id_11 | Name | dedup_bam_PE rep1 | Thread | thread_20 | PID | 50276 | | OK | false | Exit Code | 1 | Retries | | State | ERROR | Dep. | ERROR | Cpus | 1 | Mem | | | Start | 2016-05-12 23:30:48 | End | 2016-05-12 23:30:48 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
| Dependencies | | |
# SYS command. line 217
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/users/pangwei/bds_atac/.:/users/pangwei/bds_atac/modules:/users/pangwei/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 228
echo
# SYS command. line 229
samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.bam | samtools sort -n - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark
# SYS command. line 230
echo
# SYS command. line 237
samtools fixmate -r /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 238
samtools view -F 1804 -f 2 -u /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt
# SYS command. line 239
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 243
export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"
# SYS command. line 244
export MAX_JAVA_MEM="12G"
# SYS command. line 247
if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
else \
java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
INPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam" \
METRICS_FILE="/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
fi
# SYS command. line 265
mv /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 267
samtools view -F 1804 -f 2 -b /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 269
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam
# SYS command. line 271
if [ "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam.bai" != "/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bai" ]; then \
cp /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam.bai /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bai; \
fi
# SYS command. line 275
samtools flagstat /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.bam > /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.flagstat.qc
# SYS command. line 286
samtools sort -n /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp
# SYS command. line 287
bedtools bamtobed -bedpe -i /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam | \
awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
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{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/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/qc/rep1/ATAC7-trimmed-pair1.trim.PE2SE.nodup.pbc.qc
# SYS command. line 291
rm /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam.tmp.bam
# SYS command. line 293
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.filt.bam
# SYS command. line 294
rm -f /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC7+8/align/rep1/ATAC7-trimmed-pair1.trim.PE2SE.dupmark.bam
--------------------Stdout--------------------
--------------------Stderr--------------------
Error: Unable to access jarfile /picard.jar
|