| Script file | /srv/scratch/annashch/bds_atac/atac.bds |
|---|---|
| Program ID | atac.bds.20160517_222204_480 |
| Start time | 2016-05-17 22:22:04 |
| Run time | 00:01:10.769 |
| Tasks executed | 2 |
| Tasks failed | 2 |
| Tasks failed names | ataqc rep2 ataqc rep1 |
| Arguments* | [-out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq] |
| System* | local |
| Cpus* | 1 |
| Exit value | 1 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | |
| thread_21 | thread_Root | |
| thread_20 | thread_Root | |
| thread_39 | thread_Root | atac.bds.20160517_222204_480_parallel_39/task.atac.ataqc_rep2.line_847.id_15 |
| thread_38 | thread_Root | atac.bds.20160517_222204_480_parallel_38/task.atac.ataqc_rep1.line_847.id_14 |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# SYS command. line 849
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 853
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 855
cd /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2
# SYS command. line 857
/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2 \
--outdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2 \
--outprefix 3hr_rep3_merged_R1.trim.PE2SE \
--genome hg19 \
--ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
--tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
--dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
--blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
--enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
--reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
--meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
--pbc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz --fastq2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz \
--alignedbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
--bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
--naive_overlap_peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
--idr_peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH Traceback (most recent call last): File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1519, in | ||||||||||||||||||||||||||||||||||||||||
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# SYS command. line 849
if [[ -f $(which activate) ]]; then source activate bds_atac; fi; export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;
# SYS command. line 853
export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"
# SYS command. line 855
cd /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1
# SYS command. line 857
/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
--workdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1 \
--outdir /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1 \
--outprefix 3hr_rep2_merged_R1.trim.PE2SE \
--genome hg19 \
--ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
--tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
--dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
--blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
--enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
--reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
--meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
--pbc /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc\
--fastq1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz --fastq2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz \
--alignedbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam \
--alignmentlog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log \
--coordsortbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.srt.bam \
--duplog /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc \
--finalbam /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam \
--finalbed /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
--bigwig /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
--peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
--naive_overlap_peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
--idr_peaks /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz
--------------------Stderr-------------------- discarding /software/miniconda3/bin from PATH prepending /software/miniconda3/envs/bds_atac/bin to PATH Traceback (most recent call last): File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1519, in |
| Type | Name | Value |
|---|---|---|
| string | _ | /bin/sh |
| string | _JAVA_OPTIONS | -Xms256M -Xmx512M -XX:ParallelGCThreads=1 |
| bool | allowEmpty | false |
| string[] | args | [-out_dir, /srv/scratch/annashch/stemcells/het/output/4x_experiments/UnplacedChroms_noMultiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq] |
| string | BASSETDIR | /srv/scratch/annashch/Basset |
| bool | canFail | false |
| int | cpus | 1 |
| int | cpusLocal | 48 |
| string | CRC | /srv/scratch/annashch/crc |
| int | day | 86400 |
| string | DEEPLEARN_SCRIPTS_DIR | /srv/scratch/annashch/deeplearning_avanti |
| string | DEEPLIFT_DIR | /srv/scratch/annashch/deeplift/deeplift |
| real | E | 2.718281828459045 |
| string | EIGEN | /mnt/lab_data/montgomery/shared/Eigen |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/annashch/enhancer_prediction_code |
| int | G | 1073741824 |
| string | HOME | /users/annashch/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /users/annashch/keras |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1091_nRCEqi |
| string | LANG | en_US.UTF-8 |
| string | LD_LIBRARY_PATH | /lib/x86_64-linux-gnu:/usr/local/cudnn/lib64: |
| string | LOADEDMODULES | |
| string | LOGNAME | annashch |
| string | LUACPATH | /srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src: |
| string | LUAPATH | /srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src: |
| int | M | 1048576 |
| string | /var/mail/annashch | |
| string | MALLOC_ARENA_MAX | 4 |
| string | MAX_JAVA_MEM | 20G |
| 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 | node | |
| int | P | 1125899906842624 |
| string | PATH | /srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin |
| real | PI | 3.141592653589793 |
| string | ppwd | /srv/scratch/annashch/output |
| string | programName | atac.bds |
| string | programPath | /srv/scratch/annashch/bds_atac/atac.bds |
| string | PWD | /srv/scratch/annashch/output |
| string | PYTHONPATH | /users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/keras:/srv/scratch/annashch/Basset/src: |
| string | QT_QPA_PLATFORMTHEME | appmenu-qt5 |
| string | queue | |
| int | retry | 0 |
| string | SHELL | /bin/bash |
| string | SHLVL | 2 |
| string | SSH_CLIENT | 171.65.76.147 42019 22 |
| string | SSH_CONNECTION | 171.65.76.147 42019 171.65.76.162 22 |
| string | SSH_TTY | /dev/pts/128 |
| string | STY | 7061.pts-128.kali |
| string | system | local |
| 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#57:co#205: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:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{||}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:Km=\\E[M:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:\\\n\t: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:F3=\\E[1;2P:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:\\\n\t:F7=\\E[15;2~:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=:\\\n\t:K2=\\EOE:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:*4=\\E[3;2~:\\\n\t:*7=\\E[1;2F:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:\\\n\t:%e=\\E[5;2~:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:\\\n\t:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:\\\n\t:kd=\\EOB:kr=\\EOC:kl=\\EOD:km: |
| int | timeout | -1 |
| string | USER | annashch |
| string | UTIL_SCRIPTS_DIR | /srv/scratch/annashch/av_scripts |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | WINDOW | 0 |
| string | XDG_RUNTIME_DIR | /run/user/1091 |
| string | XDG_SESSION_ID | 896 |