| Script file | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/chipseq.bds |
|---|---|
| Program ID | chipseq.bds.20161006_144749_176 |
| Start time | 2016-10-06 14:47:49 |
| Run time | 14:17:30.283 |
| Tasks executed | 2 |
| Tasks failed | 0 |
| Tasks failed names | |
| Arguments* | [-title, ZF11, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.nodup.tagAlign.gz, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $] |
| System* | local |
| Cpus* | -1 |
| Exit value | 0 |
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20161006_144749_176/task.callpeak_spp.spp_rep1.line_54.id_10 chipseq.bds.20161006_144749_176/task.graphviz.report.line_97.id_11 |
| thread_42 | thread_Root | |
| thread_43 | thread_Root | |
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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# SYS command. line 56
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 0 $$
# SYS command. line 59
if [ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]; then RUN_SPP=$(which run_spp_nodups.R); \
else RUN_SPP=$(which run_spp.R); \
fi
# SYS command. line 63
Rscript ${RUN_SPP} -c=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz -p=1 -i=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.nodup.tagAlign.gz \
-npeak=300000 -odir=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1 -speak=125 -savr -savp -rf -out=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore
# SYS command. line 67
zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | awk 'BEGIN{OFS="\t"}{ if ($2<0) $2=0; print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' | gzip -f -c > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz
# SYS command. line 69
rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz
# SYS command. line 71
mv /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign.pdf /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.pdf
# SYS command. line 74
if [ $(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz | wc -l ) == "0" ]; then rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz; fi
# SYS command. line 77
if [ ! -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.regionPeak.gz ]; then error_in_spp_output_peak_does_not_exist; fi
# SYS command. line 79
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
--------------------Stdout--------------------
40047 (process ID) old priority 0, new priority 0
################
ChIP data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz
Control data: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.nodup.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 125
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: 1
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1
narrowPeak output file name: NA
regionPeak output file name: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_VS_mousePrimaryBCellInput.nodup.tagAlign.regionPeak
Rdata filename: NA
plot pdf filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign.pdf
result filename: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/peak/spp/rep1/ZF11_allReps.nodup.tagAlign_x_mousePrimaryBCellInput.nodup.tagAlign.ccscore
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz
opened /tmp/RtmpkMxfja/ZF11_allReps.nodup.tagAlign9ebf44c5af14
done. read 30207286 fragments
ChIP data read length 50
[1] TRUE
Reading Control tagAlign/BAM file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.nodup.tagAlign.gz
opened /tmp/RtmpkMxfja/mousePrimaryBCellInput.nodup.tagAlign9ebf2ce7188f
done. read 15331612 fragments
Control data read length 36
Calculating peak characteristics
Minimum cross-correlation value 0.3042838
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.450586479744112
Top 3 estimates for fragment length 125
Window half size 375
Phantom peak location 55
Phantom peak Correlation 0.4259703
Normalized Strand cross-correlation coefficient (NSC) 1.48081
Relative Strand Cross correlation Coefficient (RSC) 1.202292
Phantom Peak Quality Tag 1
null device
1
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.7116029 excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 1.405278 excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.00003
Detected 1038258 peaks
Task has finished (51440 seconds).
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
Loading required package: caTools
There were 23 warnings (use warnings() to see them)
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# SYS command. line 98
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 0 $$
# SYS command. line 99
dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/report/ZF11_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/report/ZF11_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/report/ZF11_workflow.svg" # to suppress dot font error (exit code=1)
--------------------Stdout-------------------- 54444 (process ID) old priority 0, new priority 0 --------------------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, ZF11, -nth, 5, -no_pseudo_rep, -macs2_for_pooled_rep_only, -species, mm10, -url_base, http://mitra.stanford.edu/kundaje/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out, -tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/ZF11/out/align/rep1/ZF11_allReps.nodup.tagAlign.gz, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/InputData/mousePrimaryBCellInput.nodup.tagAlign.gz, -gensz, mm, -chrsz, /mnt/data/annotations/by_organism/mouse/mm10/mm10.male.chrom.sizes, $] |
| bool | canFail | false |
| int | cpus | -1 |
| int | cpusLocal | 56 |
| int | day | 86400 |
| string | DEEPLIFT_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift |
| string | DISPLAY | localhost:12.0 |
| real | E | 2.718281828459045 |
| string | ENHANCER_SCRIPTS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/ |
| int | G | 1073741824 |
| string | HOME | /users/imk1/ |
| int | hour | 3600 |
| int | K | 1024 |
| string | KERAS_DIR | /srv/scratch/imk1/TFBindingPredictionProject/src/keras |
| string | KRB5CCNAME | FILE:/tmp/krb5cc_1048_rUZelg |
| string | LANG | en_US.UTF-8 |
| string | LOADEDMODULES | |
| string | LOGNAME | imk1 |
| int | M | 1048576 |
| string | /var/mail/imk1 | |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULE_VERSION | 3.2.10 |
| string | MODULE_VERSION_STACK | 3.2.10 |
| string | MODULEPATH | /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles |
| string | MODULESHOME | /software/env_module/3.2.10 |
| string | 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/:/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:/snap/bin:/software/miniconda3/bin:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect |
| string | PERL5LIB | /users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5 |
| string | PERL_LOCAL_LIB_ROOT | /users/imk1/perl5:/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/ZF11 |
| 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/ZF11 |
| 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 | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_CLIENT | 171.65.77.8 51178 22 |
| string | SSH_CONNECTION | 171.65.77.8 51178 171.65.76.63 22 |
| string | SSH_TTY | /dev/pts/18 |
| string | STY | 39024.ZF11.BDS |
| 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#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 |