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 | 109868 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 12:01:18 | End | 2016-05-16 13:18:35 | Elapsed | 01:17:17 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair2.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-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/ATAC1+2/align/rep1
# SYS command. line 62
$(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC1/ATAC1-trimmed-pair2.fastq.gz
# SYS command. line 63
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.fastq
# SYS command. line 64
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair2.trim.fastq
--------------------Stdout--------------------
ATAC1-trimmed-pair1.trim.fastq
ATAC1-trimmed-pair2.trim.fastq
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
46630848 sequences total
20180878 sequences trimmed with 0 mismatches
1793873 sequences trimmed with 1 mismatch
22 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 | 109873 | | OK | true | Exit Code | 0 | Retries | | State | FINISHED | Dep. | OK | Cpus | 1 | Mem | | | Start | 2016-05-16 12:01:18 | End | 2016-05-16 14:12:38 | Elapsed | 02:11:20 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair1.fastq.gz
/srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair2.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-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/ATAC1+2/align/rep2
# SYS command. line 62
$(which trimAdapters.py) -a /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair1.fastq.gz -b /srv/scratch/pangwei/mesoderm/data/ATACseq/ATAC2/ATAC2-trimmed-pair2.fastq.gz
# SYS command. line 63
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.fastq
# SYS command. line 64
gzip /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair2.trim.fastq
--------------------Stdout--------------------
ATAC2-trimmed-pair1.trim.fastq
ATAC2-trimmed-pair2.trim.fastq
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
75912589 sequences total
27962610 sequences trimmed with 0 mismatches
2647058 sequences trimmed with 1 mismatch
20 mean number of bases trimmed for reads requiring trimming
|
Num | 3 | ID | task.align_bowtie2.bowtie2_PE_rep1.line_133.id_8 | Name | bowtie2_PE rep1 | Thread | thread_20 | PID | 111345 | | OK | false | Exit Code | 0 | Retries | | State | RUNNING | Dep. | WAIT | Cpus | 2 | Mem | | | Start | 2016-05-16 13:18:36 | End | 2016-05-16 13:18:36 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair2.trim.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-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/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep1/ATAC1-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE
# SYS command. line 142
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep1/ATAC1-trimmed-pair1.trim.PE2SE.bam
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|
Num | 4 | ID | task.align_bowtie2.bowtie2_PE_rep2.line_133.id_9 | Name | bowtie2_PE rep2 | Thread | thread_21 | PID | 115358 | | OK | false | Exit Code | 0 | Retries | | State | RUNNING | Dep. | WAIT | Cpus | 2 | Mem | | | Start | 2016-05-16 14:12:39 | End | 2016-05-16 14:12:39 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.fastq.gz
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair2.trim.fastq.gz
| Output files | /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam
/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-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/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.fastq.gz -2 /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair2.trim.fastq.gz 2>/srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/qc/rep2/ATAC2-trimmed-pair1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE
# SYS command. line 142
samtools index /srv/scratch/pangwei/mesoderm/bulk-atac/output-hg19-scidata/ATAC1+2/align/rep2/ATAC2-trimmed-pair1.trim.PE2SE.bam
--------------------Stderr--------------------
discarding /users/pangwei/anaconda3/bin from PATH
prepending /users/pangwei/anaconda3/envs/bds_atac/bin to PATH
|