Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_183741_319
Start time	2017-04-13 18:37:41
Run time	00:38:58.071
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZBTB26_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -histone, $]
System*	sge
Cpus*	-1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_pooled_rep.line_155.id_10 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_ppr1.line_155.id_11 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_ppr2.line_155.id_12 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_rep1.line_155.id_13 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_14 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_15 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_rep2.line_155.id_16 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_rep2_pr1.line_155.id_17 chipseq.bds.20170413_183741_319/task.callpeak_macs2.macs2_g_b_rep2_pr2.line_155.id_18 chipseq.bds.20170413_183741_319/task.callpeak_naive_overlap.naive_overlap.line_143.id_19 chipseq.bds.20170413_183741_319/task.callpeak_naive_overlap.naive_overlap.line_143.id_20 chipseq.bds.20170413_183741_319/task.report.peak2hammock.line_361.id_23 chipseq.bds.20170413_183741_319/task.graphviz.report.line_97.id_24
thread_43	thread_Root
thread_42	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_g_b_pooled_rep.line_155.id_10
Name	macs2 g/b pooled_rep
Thread	thread_Root
PID	46974

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:37:54
End	2017-04-13 19:09:38
Elapsed	00:31:43
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 238 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
14508 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 238 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:19:  1000000 
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INFO  @ Thu, 13 Apr 2017 18:38:37:  10000000 
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INFO  @ Thu, 13 Apr 2017 18:40:37:  70000000 
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INFO  @ Thu, 13 Apr 2017 18:42:17:  120000000 
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INFO  @ Thu, 13 Apr 2017 18:42:37:  130000000 
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INFO  @ Thu, 13 Apr 2017 18:42:55:  139000000 
INFO  @ Thu, 13 Apr 2017 18:42:57:  140000000 
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INFO  @ Thu, 13 Apr 2017 18:43:13:  148000000 
INFO  @ Thu, 13 Apr 2017 18:43:15:  149000000 
INFO  @ Thu, 13 Apr 2017 18:43:17:  150000000 
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INFO  @ Thu, 13 Apr 2017 18:43:38:  160000000 
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INFO  @ Thu, 13 Apr 2017 18:43:58:  170000000 
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INFO  @ Thu, 13 Apr 2017 18:44:04:  173000000 
INFO  @ Thu, 13 Apr 2017 18:44:06:  174000000 
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INFO  @ Thu, 13 Apr 2017 18:44:18:  180000000 
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INFO  @ Thu, 13 Apr 2017 18:44:39:  190000000 
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INFO  @ Thu, 13 Apr 2017 18:44:57:  199000000 
INFO  @ Thu, 13 Apr 2017 18:44:59:  200000000 
INFO  @ Thu, 13 Apr 2017 18:45:01:  201000000 
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INFO  @ Thu, 13 Apr 2017 18:45:19:  210000000 
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INFO  @ Thu, 13 Apr 2017 18:45:35:  218000000 
INFO  @ Thu, 13 Apr 2017 18:45:37:  219000000 
INFO  @ Thu, 13 Apr 2017 18:45:59: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:46:01:  1000000 
INFO  @ Thu, 13 Apr 2017 18:46:03:  2000000 
INFO  @ Thu, 13 Apr 2017 18:46:05:  3000000 
INFO  @ Thu, 13 Apr 2017 18:46:07:  4000000 
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INFO  @ Thu, 13 Apr 2017 18:46:10:  6000000 
INFO  @ Thu, 13 Apr 2017 18:46:12:  7000000 
INFO  @ Thu, 13 Apr 2017 18:46:14:  8000000 
INFO  @ Thu, 13 Apr 2017 18:46:16:  9000000 
INFO  @ Thu, 13 Apr 2017 18:46:18:  10000000 
INFO  @ Thu, 13 Apr 2017 18:46:20:  11000000 
INFO  @ Thu, 13 Apr 2017 18:46:22:  12000000 
INFO  @ Thu, 13 Apr 2017 18:46:23:  13000000 
INFO  @ Thu, 13 Apr 2017 18:46:25:  14000000 
INFO  @ Thu, 13 Apr 2017 18:46:27:  15000000 
INFO  @ Thu, 13 Apr 2017 18:46:29:  16000000 
INFO  @ Thu, 13 Apr 2017 18:46:31:  17000000 
INFO  @ Thu, 13 Apr 2017 18:46:33:  18000000 
INFO  @ Thu, 13 Apr 2017 18:46:35:  19000000 
INFO  @ Thu, 13 Apr 2017 18:46:36:  20000000 
INFO  @ Thu, 13 Apr 2017 18:46:38:  21000000 
INFO  @ Thu, 13 Apr 2017 18:46:40:  22000000 
INFO  @ Thu, 13 Apr 2017 18:46:42:  23000000 
INFO  @ Thu, 13 Apr 2017 18:46:44:  24000000 
INFO  @ Thu, 13 Apr 2017 18:46:46:  25000000 
INFO  @ Thu, 13 Apr 2017 18:46:48:  26000000 
INFO  @ Thu, 13 Apr 2017 18:46:50:  27000000 
INFO  @ Thu, 13 Apr 2017 18:46:52:  28000000 
INFO  @ Thu, 13 Apr 2017 18:46:53:  29000000 
INFO  @ Thu, 13 Apr 2017 18:46:55:  30000000 
INFO  @ Thu, 13 Apr 2017 18:46:57:  31000000 
INFO  @ Thu, 13 Apr 2017 18:46:59:  32000000 
INFO  @ Thu, 13 Apr 2017 18:47:01:  33000000 
INFO  @ Thu, 13 Apr 2017 18:47:03:  34000000 
INFO  @ Thu, 13 Apr 2017 18:47:05:  35000000 
INFO  @ Thu, 13 Apr 2017 18:47:07:  36000000 
INFO  @ Thu, 13 Apr 2017 18:47:09:  37000000 
INFO  @ Thu, 13 Apr 2017 18:47:11:  38000000 
INFO  @ Thu, 13 Apr 2017 18:47:12:  39000000 
INFO  @ Thu, 13 Apr 2017 18:47:14:  40000000 
INFO  @ Thu, 13 Apr 2017 18:47:16:  41000000 
INFO  @ Thu, 13 Apr 2017 18:47:18:  42000000 
INFO  @ Thu, 13 Apr 2017 18:47:20:  43000000 
INFO  @ Thu, 13 Apr 2017 18:47:22:  44000000 
INFO  @ Thu, 13 Apr 2017 18:47:24:  45000000 
INFO  @ Thu, 13 Apr 2017 18:47:26:  46000000 
INFO  @ Thu, 13 Apr 2017 18:47:27:  47000000 
INFO  @ Thu, 13 Apr 2017 18:47:29:  48000000 
INFO  @ Thu, 13 Apr 2017 18:47:31:  49000000 
INFO  @ Thu, 13 Apr 2017 18:47:33:  50000000 
INFO  @ Thu, 13 Apr 2017 18:47:35:  51000000 
INFO  @ Thu, 13 Apr 2017 18:47:37:  52000000 
INFO  @ Thu, 13 Apr 2017 18:47:39:  53000000 
INFO  @ Thu, 13 Apr 2017 18:47:41:  54000000 
INFO  @ Thu, 13 Apr 2017 18:47:42:  55000000 
INFO  @ Thu, 13 Apr 2017 18:47:44:  56000000 
INFO  @ Thu, 13 Apr 2017 18:47:47:  57000000 
INFO  @ Thu, 13 Apr 2017 18:47:49:  58000000 
INFO  @ Thu, 13 Apr 2017 18:47:51:  59000000 
INFO  @ Thu, 13 Apr 2017 18:47:52:  60000000 
INFO  @ Thu, 13 Apr 2017 18:47:54:  61000000 
INFO  @ Thu, 13 Apr 2017 18:47:56:  62000000 
INFO  @ Thu, 13 Apr 2017 18:47:58:  63000000 
INFO  @ Thu, 13 Apr 2017 18:48:00:  64000000 
INFO  @ Thu, 13 Apr 2017 18:48:02:  65000000 
INFO  @ Thu, 13 Apr 2017 18:48:04:  66000000 
INFO  @ Thu, 13 Apr 2017 18:48:06:  67000000 
INFO  @ Thu, 13 Apr 2017 18:48:07:  68000000 
INFO  @ Thu, 13 Apr 2017 18:48:09:  69000000 
INFO  @ Thu, 13 Apr 2017 18:48:11:  70000000 
INFO  @ Thu, 13 Apr 2017 18:48:13:  71000000 
INFO  @ Thu, 13 Apr 2017 18:48:15:  72000000 
INFO  @ Thu, 13 Apr 2017 18:48:17:  73000000 
INFO  @ Thu, 13 Apr 2017 18:48:19:  74000000 
INFO  @ Thu, 13 Apr 2017 18:48:21:  75000000 
INFO  @ Thu, 13 Apr 2017 18:48:22:  76000000 
INFO  @ Thu, 13 Apr 2017 18:48:24:  77000000 
INFO  @ Thu, 13 Apr 2017 18:48:26:  78000000 
INFO  @ Thu, 13 Apr 2017 18:48:28:  79000000 
INFO  @ Thu, 13 Apr 2017 18:48:30:  80000000 
INFO  @ Thu, 13 Apr 2017 18:48:32:  81000000 
INFO  @ Thu, 13 Apr 2017 18:48:34:  82000000 
INFO  @ Thu, 13 Apr 2017 18:48:35:  83000000 
INFO  @ Thu, 13 Apr 2017 18:48:37:  84000000 
INFO  @ Thu, 13 Apr 2017 18:48:40:  85000000 
INFO  @ Thu, 13 Apr 2017 18:48:42:  86000000 
INFO  @ Thu, 13 Apr 2017 18:48:43:  87000000 
INFO  @ Thu, 13 Apr 2017 18:48:45:  88000000 
INFO  @ Thu, 13 Apr 2017 18:48:47:  89000000 
INFO  @ Thu, 13 Apr 2017 18:48:49:  90000000 
INFO  @ Thu, 13 Apr 2017 18:48:51:  91000000 
INFO  @ Thu, 13 Apr 2017 18:48:53:  92000000 
INFO  @ Thu, 13 Apr 2017 18:48:55:  93000000 
INFO  @ Thu, 13 Apr 2017 18:48:56:  94000000 
INFO  @ Thu, 13 Apr 2017 18:48:58:  95000000 
INFO  @ Thu, 13 Apr 2017 18:49:00:  96000000 
INFO  @ Thu, 13 Apr 2017 18:49:02:  97000000 
INFO  @ Thu, 13 Apr 2017 18:49:04:  98000000 
INFO  @ Thu, 13 Apr 2017 18:49:05:  99000000 
INFO  @ Thu, 13 Apr 2017 18:49:08: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:49:08: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:49:08: #1  total tags in treatment: 219735318 
INFO  @ Thu, 13 Apr 2017 18:49:08: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:49:08: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:49:08: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:49:08: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:49:08: #2 Use 238 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:49:08: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:49:08: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:49:08: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:02:58: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:09:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:09:34: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:09:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:09:35: Done!

Num	2
ID	task.callpeak_macs2.macs2_g_b_ppr1.line_155.id_11
Name	macs2 g/b ppr1
Thread	thread_Root
PID	46980

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:37:56
End	2017-04-13 18:57:05
Elapsed	00:19:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 238 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
14281 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 238 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:24:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:30:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:32:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:38:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  25000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  26000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  56000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  57000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  58000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  59000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  60000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  61000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  62000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  63000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  72000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  73000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  74000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  75000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  77000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  78000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  79000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  80000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  81000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  82000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  83000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  84000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  85000000 
INFO  @ Thu, 13 Apr 2017 18:40:34:  86000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  87000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  88000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  89000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  90000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  91000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  92000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  93000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  94000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  95000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  96000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  97000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  98000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  99000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  100000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  101000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  102000000 
INFO  @ Thu, 13 Apr 2017 18:41:02:  103000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  104000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  105000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  106000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  107000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  108000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  109000000 
INFO  @ Thu, 13 Apr 2017 18:41:21: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:41:23:  1000000 
INFO  @ Thu, 13 Apr 2017 18:41:24:  2000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  3000000 
INFO  @ Thu, 13 Apr 2017 18:41:28:  4000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  5000000 
INFO  @ Thu, 13 Apr 2017 18:41:31:  6000000 
INFO  @ Thu, 13 Apr 2017 18:41:32:  7000000 
INFO  @ Thu, 13 Apr 2017 18:41:34:  8000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  9000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  10000000 
INFO  @ Thu, 13 Apr 2017 18:41:38:  11000000 
INFO  @ Thu, 13 Apr 2017 18:41:40:  12000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  13000000 
INFO  @ Thu, 13 Apr 2017 18:41:43:  14000000 
INFO  @ Thu, 13 Apr 2017 18:41:44:  15000000 
INFO  @ Thu, 13 Apr 2017 18:41:46:  16000000 
INFO  @ Thu, 13 Apr 2017 18:41:48:  17000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  18000000 
INFO  @ Thu, 13 Apr 2017 18:41:51:  19000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  20000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  21000000 
INFO  @ Thu, 13 Apr 2017 18:41:55:  22000000 
INFO  @ Thu, 13 Apr 2017 18:41:57:  23000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  24000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  25000000 
INFO  @ Thu, 13 Apr 2017 18:42:01:  26000000 
INFO  @ Thu, 13 Apr 2017 18:42:03:  27000000 
INFO  @ Thu, 13 Apr 2017 18:42:04:  28000000 
INFO  @ Thu, 13 Apr 2017 18:42:06:  29000000 
INFO  @ Thu, 13 Apr 2017 18:42:07:  30000000 
INFO  @ Thu, 13 Apr 2017 18:42:09:  31000000 
INFO  @ Thu, 13 Apr 2017 18:42:10:  32000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  33000000 
INFO  @ Thu, 13 Apr 2017 18:42:13:  34000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  35000000 
INFO  @ Thu, 13 Apr 2017 18:42:16:  36000000 
INFO  @ Thu, 13 Apr 2017 18:42:18:  37000000 
INFO  @ Thu, 13 Apr 2017 18:42:19:  38000000 
INFO  @ Thu, 13 Apr 2017 18:42:21:  39000000 
INFO  @ Thu, 13 Apr 2017 18:42:22:  40000000 
INFO  @ Thu, 13 Apr 2017 18:42:24:  41000000 
INFO  @ Thu, 13 Apr 2017 18:42:25:  42000000 
INFO  @ Thu, 13 Apr 2017 18:42:27:  43000000 
INFO  @ Thu, 13 Apr 2017 18:42:29:  44000000 
INFO  @ Thu, 13 Apr 2017 18:42:30:  45000000 
INFO  @ Thu, 13 Apr 2017 18:42:31:  46000000 
INFO  @ Thu, 13 Apr 2017 18:42:33:  47000000 
INFO  @ Thu, 13 Apr 2017 18:42:34:  48000000 
INFO  @ Thu, 13 Apr 2017 18:42:36:  49000000 
INFO  @ Thu, 13 Apr 2017 18:42:37:  50000000 
INFO  @ Thu, 13 Apr 2017 18:42:39:  51000000 
INFO  @ Thu, 13 Apr 2017 18:42:41:  52000000 
INFO  @ Thu, 13 Apr 2017 18:42:42:  53000000 
INFO  @ Thu, 13 Apr 2017 18:42:44:  54000000 
INFO  @ Thu, 13 Apr 2017 18:42:45:  55000000 
INFO  @ Thu, 13 Apr 2017 18:42:47:  56000000 
INFO  @ Thu, 13 Apr 2017 18:42:48:  57000000 
INFO  @ Thu, 13 Apr 2017 18:42:50:  58000000 
INFO  @ Thu, 13 Apr 2017 18:42:51:  59000000 
INFO  @ Thu, 13 Apr 2017 18:42:53:  60000000 
INFO  @ Thu, 13 Apr 2017 18:42:54:  61000000 
INFO  @ Thu, 13 Apr 2017 18:42:56:  62000000 
INFO  @ Thu, 13 Apr 2017 18:42:57:  63000000 
INFO  @ Thu, 13 Apr 2017 18:42:59:  64000000 
INFO  @ Thu, 13 Apr 2017 18:43:01:  65000000 
INFO  @ Thu, 13 Apr 2017 18:43:02:  66000000 
INFO  @ Thu, 13 Apr 2017 18:43:04:  67000000 
INFO  @ Thu, 13 Apr 2017 18:43:05:  68000000 
INFO  @ Thu, 13 Apr 2017 18:43:07:  69000000 
INFO  @ Thu, 13 Apr 2017 18:43:08:  70000000 
INFO  @ Thu, 13 Apr 2017 18:43:10:  71000000 
INFO  @ Thu, 13 Apr 2017 18:43:11:  72000000 
INFO  @ Thu, 13 Apr 2017 18:43:12:  73000000 
INFO  @ Thu, 13 Apr 2017 18:43:14:  74000000 
INFO  @ Thu, 13 Apr 2017 18:43:15:  75000000 
INFO  @ Thu, 13 Apr 2017 18:43:17:  76000000 
INFO  @ Thu, 13 Apr 2017 18:43:18:  77000000 
INFO  @ Thu, 13 Apr 2017 18:43:20:  78000000 
INFO  @ Thu, 13 Apr 2017 18:43:22:  79000000 
INFO  @ Thu, 13 Apr 2017 18:43:23:  80000000 
INFO  @ Thu, 13 Apr 2017 18:43:25:  81000000 
INFO  @ Thu, 13 Apr 2017 18:43:26:  82000000 
INFO  @ Thu, 13 Apr 2017 18:43:28:  83000000 
INFO  @ Thu, 13 Apr 2017 18:43:29:  84000000 
INFO  @ Thu, 13 Apr 2017 18:43:31:  85000000 
INFO  @ Thu, 13 Apr 2017 18:43:32:  86000000 
INFO  @ Thu, 13 Apr 2017 18:43:34:  87000000 
INFO  @ Thu, 13 Apr 2017 18:43:35:  88000000 
INFO  @ Thu, 13 Apr 2017 18:43:37:  89000000 
INFO  @ Thu, 13 Apr 2017 18:43:38:  90000000 
INFO  @ Thu, 13 Apr 2017 18:43:40:  91000000 
INFO  @ Thu, 13 Apr 2017 18:43:41:  92000000 
INFO  @ Thu, 13 Apr 2017 18:43:43:  93000000 
INFO  @ Thu, 13 Apr 2017 18:43:44:  94000000 
INFO  @ Thu, 13 Apr 2017 18:43:46:  95000000 
INFO  @ Thu, 13 Apr 2017 18:43:48:  96000000 
INFO  @ Thu, 13 Apr 2017 18:43:49:  97000000 
INFO  @ Thu, 13 Apr 2017 18:43:51:  98000000 
INFO  @ Thu, 13 Apr 2017 18:43:52:  99000000 
INFO  @ Thu, 13 Apr 2017 18:43:54: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:43:54: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:43:54: #1  total tags in treatment: 109867660 
INFO  @ Thu, 13 Apr 2017 18:43:54: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:43:54: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:43:54: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:43:54: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:43:54: #2 Use 238 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:43:54: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:43:54: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:43:54: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:51:29: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:57:00: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:57:01: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:57:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:57:02: Done!

Num	3
ID	task.callpeak_macs2.macs2_g_b_ppr2.line_155.id_12
Name	macs2 g/b ppr2
Thread	thread_Root
PID	46982

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:37:57
End	2017-04-13 18:54:19
Elapsed	00:16:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 238 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
48812 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 238 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  56000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  57000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  58000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  72000000 
INFO  @ Thu, 13 Apr 2017 18:40:22:  73000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  74000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  75000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  77000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  78000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  79000000 
INFO  @ Thu, 13 Apr 2017 18:40:34:  80000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  81000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  82000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  83000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  84000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  85000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  86000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  87000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  88000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  89000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  90000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  91000000 
INFO  @ Thu, 13 Apr 2017 18:40:53:  92000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  93000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  94000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  95000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  96000000 
INFO  @ Thu, 13 Apr 2017 18:41:01:  97000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  98000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:07:  100000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  101000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  102000000 
INFO  @ Thu, 13 Apr 2017 18:41:12:  103000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  104000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  105000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  106000000 
INFO  @ Thu, 13 Apr 2017 18:41:18:  107000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  108000000 
INFO  @ Thu, 13 Apr 2017 18:41:21:  109000000 
INFO  @ Thu, 13 Apr 2017 18:41:30: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:41:31:  1000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  2000000 
INFO  @ Thu, 13 Apr 2017 18:41:34:  3000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  4000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  5000000 
INFO  @ Thu, 13 Apr 2017 18:41:38:  6000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  7000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  8000000 
INFO  @ Thu, 13 Apr 2017 18:41:42:  9000000 
INFO  @ Thu, 13 Apr 2017 18:41:44:  10000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  11000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  12000000 
INFO  @ Thu, 13 Apr 2017 18:41:48:  13000000 
INFO  @ Thu, 13 Apr 2017 18:41:50:  14000000 
INFO  @ Thu, 13 Apr 2017 18:41:51:  15000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  16000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  17000000 
INFO  @ Thu, 13 Apr 2017 18:41:55:  18000000 
INFO  @ Thu, 13 Apr 2017 18:41:57:  19000000 
INFO  @ Thu, 13 Apr 2017 18:41:59:  20000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  21000000 
INFO  @ Thu, 13 Apr 2017 18:42:01:  22000000 
INFO  @ Thu, 13 Apr 2017 18:42:03:  23000000 
INFO  @ Thu, 13 Apr 2017 18:42:04:  24000000 
INFO  @ Thu, 13 Apr 2017 18:42:06:  25000000 
INFO  @ Thu, 13 Apr 2017 18:42:07:  26000000 
INFO  @ Thu, 13 Apr 2017 18:42:08:  27000000 
INFO  @ Thu, 13 Apr 2017 18:42:10:  28000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  29000000 
INFO  @ Thu, 13 Apr 2017 18:42:13:  30000000 
INFO  @ Thu, 13 Apr 2017 18:42:14:  31000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  32000000 
INFO  @ Thu, 13 Apr 2017 18:42:17:  33000000 
INFO  @ Thu, 13 Apr 2017 18:42:18:  34000000 
INFO  @ Thu, 13 Apr 2017 18:42:20:  35000000 
INFO  @ Thu, 13 Apr 2017 18:42:21:  36000000 
INFO  @ Thu, 13 Apr 2017 18:42:22:  37000000 
INFO  @ Thu, 13 Apr 2017 18:42:24:  38000000 
INFO  @ Thu, 13 Apr 2017 18:42:25:  39000000 
INFO  @ Thu, 13 Apr 2017 18:42:26:  40000000 
INFO  @ Thu, 13 Apr 2017 18:42:28:  41000000 
INFO  @ Thu, 13 Apr 2017 18:42:29:  42000000 
INFO  @ Thu, 13 Apr 2017 18:42:31:  43000000 
INFO  @ Thu, 13 Apr 2017 18:42:32:  44000000 
INFO  @ Thu, 13 Apr 2017 18:42:33:  45000000 
INFO  @ Thu, 13 Apr 2017 18:42:35:  46000000 
INFO  @ Thu, 13 Apr 2017 18:42:36:  47000000 
INFO  @ Thu, 13 Apr 2017 18:42:38:  48000000 
INFO  @ Thu, 13 Apr 2017 18:42:39:  49000000 
INFO  @ Thu, 13 Apr 2017 18:42:40:  50000000 
INFO  @ Thu, 13 Apr 2017 18:42:42:  51000000 
INFO  @ Thu, 13 Apr 2017 18:42:43:  52000000 
INFO  @ Thu, 13 Apr 2017 18:42:45:  53000000 
INFO  @ Thu, 13 Apr 2017 18:42:46:  54000000 
INFO  @ Thu, 13 Apr 2017 18:42:48:  55000000 
INFO  @ Thu, 13 Apr 2017 18:42:49:  56000000 
INFO  @ Thu, 13 Apr 2017 18:42:50:  57000000 
INFO  @ Thu, 13 Apr 2017 18:42:52:  58000000 
INFO  @ Thu, 13 Apr 2017 18:42:53:  59000000 
INFO  @ Thu, 13 Apr 2017 18:42:55:  60000000 
INFO  @ Thu, 13 Apr 2017 18:42:56:  61000000 
INFO  @ Thu, 13 Apr 2017 18:42:57:  62000000 
INFO  @ Thu, 13 Apr 2017 18:42:59:  63000000 
INFO  @ Thu, 13 Apr 2017 18:43:00:  64000000 
INFO  @ Thu, 13 Apr 2017 18:43:02:  65000000 
INFO  @ Thu, 13 Apr 2017 18:43:03:  66000000 
INFO  @ Thu, 13 Apr 2017 18:43:04:  67000000 
INFO  @ Thu, 13 Apr 2017 18:43:06:  68000000 
INFO  @ Thu, 13 Apr 2017 18:43:07:  69000000 
INFO  @ Thu, 13 Apr 2017 18:43:09:  70000000 
INFO  @ Thu, 13 Apr 2017 18:43:10:  71000000 
INFO  @ Thu, 13 Apr 2017 18:43:11:  72000000 
INFO  @ Thu, 13 Apr 2017 18:43:13:  73000000 
INFO  @ Thu, 13 Apr 2017 18:43:14:  74000000 
INFO  @ Thu, 13 Apr 2017 18:43:16:  75000000 
INFO  @ Thu, 13 Apr 2017 18:43:17:  76000000 
INFO  @ Thu, 13 Apr 2017 18:43:19:  77000000 
INFO  @ Thu, 13 Apr 2017 18:43:20:  78000000 
INFO  @ Thu, 13 Apr 2017 18:43:21:  79000000 
INFO  @ Thu, 13 Apr 2017 18:43:23:  80000000 
INFO  @ Thu, 13 Apr 2017 18:43:24:  81000000 
INFO  @ Thu, 13 Apr 2017 18:43:26:  82000000 
INFO  @ Thu, 13 Apr 2017 18:43:27:  83000000 
INFO  @ Thu, 13 Apr 2017 18:43:29:  84000000 
INFO  @ Thu, 13 Apr 2017 18:43:30:  85000000 
INFO  @ Thu, 13 Apr 2017 18:43:32:  86000000 
INFO  @ Thu, 13 Apr 2017 18:43:34:  87000000 
INFO  @ Thu, 13 Apr 2017 18:43:35:  88000000 
INFO  @ Thu, 13 Apr 2017 18:43:37:  89000000 
INFO  @ Thu, 13 Apr 2017 18:43:38:  90000000 
INFO  @ Thu, 13 Apr 2017 18:43:39:  91000000 
INFO  @ Thu, 13 Apr 2017 18:43:41:  92000000 
INFO  @ Thu, 13 Apr 2017 18:43:42:  93000000 
INFO  @ Thu, 13 Apr 2017 18:43:44:  94000000 
INFO  @ Thu, 13 Apr 2017 18:43:45:  95000000 
INFO  @ Thu, 13 Apr 2017 18:43:47:  96000000 
INFO  @ Thu, 13 Apr 2017 18:43:48:  97000000 
INFO  @ Thu, 13 Apr 2017 18:43:49:  98000000 
INFO  @ Thu, 13 Apr 2017 18:43:51:  99000000 
INFO  @ Thu, 13 Apr 2017 18:43:52: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:43:52: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:43:52: #1  total tags in treatment: 109867658 
INFO  @ Thu, 13 Apr 2017 18:43:52: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:43:52: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:43:52: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:43:52: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:43:52: #2 Use 238 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:43:52: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:43:52: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:43:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:50:46: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:54:15: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:54:16: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:54:16: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:54:16: Done!

Num	4
ID	task.callpeak_macs2.macs2_g_b_rep1.line_155.id_13
Name	macs2 g/b rep1
Thread	thread_Root
PID	46986

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:37:59
End	2017-04-13 18:54:39
Elapsed	00:16:39
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 235 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
14283 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 235 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:24:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:32:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  56000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  57000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  58000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  59000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  72000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  73000000 
INFO  @ Thu, 13 Apr 2017 18:40:22:  74000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  75000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  77000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  78000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  79000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  80000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  81000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  82000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  83000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  84000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  85000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  86000000 
INFO  @ Thu, 13 Apr 2017 18:40:43:  87000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  88000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  89000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  90000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  91000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  92000000 
INFO  @ Thu, 13 Apr 2017 18:40:53:  93000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  94000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  95000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  96000000 
INFO  @ Thu, 13 Apr 2017 18:40:59:  97000000 
INFO  @ Thu, 13 Apr 2017 18:41:01:  98000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:04:  100000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  101000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  102000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  103000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  104000000 
INFO  @ Thu, 13 Apr 2017 18:41:12:  105000000 
INFO  @ Thu, 13 Apr 2017 18:41:14:  106000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  107000000 
INFO  @ Thu, 13 Apr 2017 18:41:17:  108000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  109000000 
INFO  @ Thu, 13 Apr 2017 18:41:21:  110000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  111000000 
INFO  @ Thu, 13 Apr 2017 18:41:24:  112000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  113000000 
INFO  @ Thu, 13 Apr 2017 18:41:27:  114000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  115000000 
INFO  @ Thu, 13 Apr 2017 18:41:30:  116000000 
INFO  @ Thu, 13 Apr 2017 18:41:32:  117000000 
INFO  @ Thu, 13 Apr 2017 18:41:34:  118000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  119000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  120000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  121000000 
INFO  @ Thu, 13 Apr 2017 18:41:40:  122000000 
INFO  @ Thu, 13 Apr 2017 18:41:42:  123000000 
INFO  @ Thu, 13 Apr 2017 18:41:44:  124000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  125000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  126000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  127000000 
INFO  @ Thu, 13 Apr 2017 18:42:00: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:42:02:  1000000 
INFO  @ Thu, 13 Apr 2017 18:42:03:  2000000 
INFO  @ Thu, 13 Apr 2017 18:42:05:  3000000 
INFO  @ Thu, 13 Apr 2017 18:42:07:  4000000 
INFO  @ Thu, 13 Apr 2017 18:42:08:  5000000 
INFO  @ Thu, 13 Apr 2017 18:42:10:  6000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  7000000 
INFO  @ Thu, 13 Apr 2017 18:42:13:  8000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  9000000 
INFO  @ Thu, 13 Apr 2017 18:42:16:  10000000 
INFO  @ Thu, 13 Apr 2017 18:42:18:  11000000 
INFO  @ Thu, 13 Apr 2017 18:42:20:  12000000 
INFO  @ Thu, 13 Apr 2017 18:42:21:  13000000 
INFO  @ Thu, 13 Apr 2017 18:42:23:  14000000 
INFO  @ Thu, 13 Apr 2017 18:42:24:  15000000 
INFO  @ Thu, 13 Apr 2017 18:42:26:  16000000 
INFO  @ Thu, 13 Apr 2017 18:42:28:  17000000 
INFO  @ Thu, 13 Apr 2017 18:42:29:  18000000 
INFO  @ Thu, 13 Apr 2017 18:42:31:  19000000 
INFO  @ Thu, 13 Apr 2017 18:42:33:  20000000 
INFO  @ Thu, 13 Apr 2017 18:42:34:  21000000 
INFO  @ Thu, 13 Apr 2017 18:42:36:  22000000 
INFO  @ Thu, 13 Apr 2017 18:42:38:  23000000 
INFO  @ Thu, 13 Apr 2017 18:42:39:  24000000 
INFO  @ Thu, 13 Apr 2017 18:42:41:  25000000 
INFO  @ Thu, 13 Apr 2017 18:42:42:  26000000 
INFO  @ Thu, 13 Apr 2017 18:42:44:  27000000 
INFO  @ Thu, 13 Apr 2017 18:42:45:  28000000 
INFO  @ Thu, 13 Apr 2017 18:42:47:  29000000 
INFO  @ Thu, 13 Apr 2017 18:42:48:  30000000 
INFO  @ Thu, 13 Apr 2017 18:42:50:  31000000 
INFO  @ Thu, 13 Apr 2017 18:42:51:  32000000 
INFO  @ Thu, 13 Apr 2017 18:42:53:  33000000 
INFO  @ Thu, 13 Apr 2017 18:42:55:  34000000 
INFO  @ Thu, 13 Apr 2017 18:42:56:  35000000 
INFO  @ Thu, 13 Apr 2017 18:42:58:  36000000 
INFO  @ Thu, 13 Apr 2017 18:42:59:  37000000 
INFO  @ Thu, 13 Apr 2017 18:43:01:  38000000 
INFO  @ Thu, 13 Apr 2017 18:43:02:  39000000 
INFO  @ Thu, 13 Apr 2017 18:43:04:  40000000 
INFO  @ Thu, 13 Apr 2017 18:43:05:  41000000 
INFO  @ Thu, 13 Apr 2017 18:43:07:  42000000 
INFO  @ Thu, 13 Apr 2017 18:43:09:  43000000 
INFO  @ Thu, 13 Apr 2017 18:43:10:  44000000 
INFO  @ Thu, 13 Apr 2017 18:43:12:  45000000 
INFO  @ Thu, 13 Apr 2017 18:43:13:  46000000 
INFO  @ Thu, 13 Apr 2017 18:43:15:  47000000 
INFO  @ Thu, 13 Apr 2017 18:43:16:  48000000 
INFO  @ Thu, 13 Apr 2017 18:43:18:  49000000 
INFO  @ Thu, 13 Apr 2017 18:43:19:  50000000 
INFO  @ Thu, 13 Apr 2017 18:43:21:  51000000 
INFO  @ Thu, 13 Apr 2017 18:43:22:  52000000 
INFO  @ Thu, 13 Apr 2017 18:43:24:  53000000 
INFO  @ Thu, 13 Apr 2017 18:43:25:  54000000 
INFO  @ Thu, 13 Apr 2017 18:43:27:  55000000 
INFO  @ Thu, 13 Apr 2017 18:43:28:  56000000 
INFO  @ Thu, 13 Apr 2017 18:43:30:  57000000 
INFO  @ Thu, 13 Apr 2017 18:43:32:  58000000 
INFO  @ Thu, 13 Apr 2017 18:43:33:  59000000 
INFO  @ Thu, 13 Apr 2017 18:43:35:  60000000 
INFO  @ Thu, 13 Apr 2017 18:43:36:  61000000 
INFO  @ Thu, 13 Apr 2017 18:43:38:  62000000 
INFO  @ Thu, 13 Apr 2017 18:43:39:  63000000 
INFO  @ Thu, 13 Apr 2017 18:43:41:  64000000 
INFO  @ Thu, 13 Apr 2017 18:43:43:  65000000 
INFO  @ Thu, 13 Apr 2017 18:43:44:  66000000 
INFO  @ Thu, 13 Apr 2017 18:43:46:  67000000 
INFO  @ Thu, 13 Apr 2017 18:43:47:  68000000 
INFO  @ Thu, 13 Apr 2017 18:43:49:  69000000 
INFO  @ Thu, 13 Apr 2017 18:43:50:  70000000 
INFO  @ Thu, 13 Apr 2017 18:43:52:  71000000 
INFO  @ Thu, 13 Apr 2017 18:43:53:  72000000 
INFO  @ Thu, 13 Apr 2017 18:43:55:  73000000 
INFO  @ Thu, 13 Apr 2017 18:43:56:  74000000 
INFO  @ Thu, 13 Apr 2017 18:43:58:  75000000 
INFO  @ Thu, 13 Apr 2017 18:43:59:  76000000 
INFO  @ Thu, 13 Apr 2017 18:44:01:  77000000 
INFO  @ Thu, 13 Apr 2017 18:44:02:  78000000 
INFO  @ Thu, 13 Apr 2017 18:44:04:  79000000 
INFO  @ Thu, 13 Apr 2017 18:44:05:  80000000 
INFO  @ Thu, 13 Apr 2017 18:44:07:  81000000 
INFO  @ Thu, 13 Apr 2017 18:44:08:  82000000 
INFO  @ Thu, 13 Apr 2017 18:44:10:  83000000 
INFO  @ Thu, 13 Apr 2017 18:44:11:  84000000 
INFO  @ Thu, 13 Apr 2017 18:44:13:  85000000 
INFO  @ Thu, 13 Apr 2017 18:44:14:  86000000 
INFO  @ Thu, 13 Apr 2017 18:44:16:  87000000 
INFO  @ Thu, 13 Apr 2017 18:44:18:  88000000 
INFO  @ Thu, 13 Apr 2017 18:44:19:  89000000 
INFO  @ Thu, 13 Apr 2017 18:44:21:  90000000 
INFO  @ Thu, 13 Apr 2017 18:44:22:  91000000 
INFO  @ Thu, 13 Apr 2017 18:44:24:  92000000 
INFO  @ Thu, 13 Apr 2017 18:44:26:  93000000 
INFO  @ Thu, 13 Apr 2017 18:44:27:  94000000 
INFO  @ Thu, 13 Apr 2017 18:44:29:  95000000 
INFO  @ Thu, 13 Apr 2017 18:44:30:  96000000 
INFO  @ Thu, 13 Apr 2017 18:44:32:  97000000 
INFO  @ Thu, 13 Apr 2017 18:44:34:  98000000 
INFO  @ Thu, 13 Apr 2017 18:44:35:  99000000 
INFO  @ Thu, 13 Apr 2017 18:44:37: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:44:37: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:44:37: #1  total tags in treatment: 127505544 
INFO  @ Thu, 13 Apr 2017 18:44:37: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:44:37: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:44:37: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:44:37: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:44:37: #2 Use 235 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:44:37: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:44:37: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:44:37: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:51:18: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:54:33: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:54:34: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:54:34: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:54:35: Done!

Num	5
ID	task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_14
Name	macs2 g/b rep1-pr1
Thread	thread_Root
PID	46991

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:38:01
End	2017-04-13 18:52:16
Elapsed	00:14:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 235 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
24548 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 235 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:19:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:30:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  25000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  26000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  56000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  57000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  58000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  59000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  60000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  61000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  62000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:01: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:40:03:  1000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  2000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  3000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  4000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  5000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  6000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  7000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  8000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  9000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  10000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  11000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  12000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  13000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  14000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  15000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  16000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  17000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  18000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  19000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  20000000 
INFO  @ Thu, 13 Apr 2017 18:40:34:  21000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  22000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  23000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  24000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  25000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  26000000 
INFO  @ Thu, 13 Apr 2017 18:40:43:  27000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  28000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  29000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  30000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  31000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  32000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  33000000 
INFO  @ Thu, 13 Apr 2017 18:40:53:  34000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  35000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  36000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  37000000 
INFO  @ Thu, 13 Apr 2017 18:40:59:  38000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  39000000 
INFO  @ Thu, 13 Apr 2017 18:41:02:  40000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  41000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  42000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  43000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  44000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  45000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  46000000 
INFO  @ Thu, 13 Apr 2017 18:41:12:  47000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  48000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  49000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  50000000 
INFO  @ Thu, 13 Apr 2017 18:41:18:  51000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  52000000 
INFO  @ Thu, 13 Apr 2017 18:41:21:  53000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  54000000 
INFO  @ Thu, 13 Apr 2017 18:41:23:  55000000 
INFO  @ Thu, 13 Apr 2017 18:41:25:  56000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  57000000 
INFO  @ Thu, 13 Apr 2017 18:41:28:  58000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  59000000 
INFO  @ Thu, 13 Apr 2017 18:41:31:  60000000 
INFO  @ Thu, 13 Apr 2017 18:41:32:  61000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  62000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  63000000 
INFO  @ Thu, 13 Apr 2017 18:41:36:  64000000 
INFO  @ Thu, 13 Apr 2017 18:41:38:  65000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  66000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  67000000 
INFO  @ Thu, 13 Apr 2017 18:41:42:  68000000 
INFO  @ Thu, 13 Apr 2017 18:41:44:  69000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  70000000 
INFO  @ Thu, 13 Apr 2017 18:41:46:  71000000 
INFO  @ Thu, 13 Apr 2017 18:41:48:  72000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  73000000 
INFO  @ Thu, 13 Apr 2017 18:41:51:  74000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  75000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  76000000 
INFO  @ Thu, 13 Apr 2017 18:41:55:  77000000 
INFO  @ Thu, 13 Apr 2017 18:41:56:  78000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  79000000 
INFO  @ Thu, 13 Apr 2017 18:41:59:  80000000 
INFO  @ Thu, 13 Apr 2017 18:42:01:  81000000 
INFO  @ Thu, 13 Apr 2017 18:42:02:  82000000 
INFO  @ Thu, 13 Apr 2017 18:42:04:  83000000 
INFO  @ Thu, 13 Apr 2017 18:42:05:  84000000 
INFO  @ Thu, 13 Apr 2017 18:42:06:  85000000 
INFO  @ Thu, 13 Apr 2017 18:42:08:  86000000 
INFO  @ Thu, 13 Apr 2017 18:42:09:  87000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  88000000 
INFO  @ Thu, 13 Apr 2017 18:42:12:  89000000 
INFO  @ Thu, 13 Apr 2017 18:42:14:  90000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  91000000 
INFO  @ Thu, 13 Apr 2017 18:42:17:  92000000 
INFO  @ Thu, 13 Apr 2017 18:42:18:  93000000 
INFO  @ Thu, 13 Apr 2017 18:42:19:  94000000 
INFO  @ Thu, 13 Apr 2017 18:42:21:  95000000 
INFO  @ Thu, 13 Apr 2017 18:42:22:  96000000 
INFO  @ Thu, 13 Apr 2017 18:42:24:  97000000 
INFO  @ Thu, 13 Apr 2017 18:42:25:  98000000 
INFO  @ Thu, 13 Apr 2017 18:42:26:  99000000 
INFO  @ Thu, 13 Apr 2017 18:42:28: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:42:28: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:42:28: #1  total tags in treatment: 63752772 
INFO  @ Thu, 13 Apr 2017 18:42:28: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:42:28: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:42:28: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:42:28: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:42:28: #2 Use 235 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:42:28: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:42:28: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:42:28: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:48:35: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:52:07: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:52:09: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:52:10: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF066ZSK.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:52:11: Done!

Num	6
ID	task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_15
Name	macs2 g/b rep1-pr2
Thread	thread_Root
PID	47019

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:52:20
End	2017-04-13 19:06:30
Elapsed	00:14:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 235 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
34641 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:52:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 235 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:52:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:52:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:52:33:  1000000 
INFO  @ Thu, 13 Apr 2017 18:52:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:52:37:  3000000 
INFO  @ Thu, 13 Apr 2017 18:52:38:  4000000 
INFO  @ Thu, 13 Apr 2017 18:52:40:  5000000 
INFO  @ Thu, 13 Apr 2017 18:52:41:  6000000 
INFO  @ Thu, 13 Apr 2017 18:52:43:  7000000 
INFO  @ Thu, 13 Apr 2017 18:52:45:  8000000 
INFO  @ Thu, 13 Apr 2017 18:52:46:  9000000 
INFO  @ Thu, 13 Apr 2017 18:52:48:  10000000 
INFO  @ Thu, 13 Apr 2017 18:52:49:  11000000 
INFO  @ Thu, 13 Apr 2017 18:52:51:  12000000 
INFO  @ Thu, 13 Apr 2017 18:52:53:  13000000 
INFO  @ Thu, 13 Apr 2017 18:52:54:  14000000 
INFO  @ Thu, 13 Apr 2017 18:52:56:  15000000 
INFO  @ Thu, 13 Apr 2017 18:52:57:  16000000 
INFO  @ Thu, 13 Apr 2017 18:52:59:  17000000 
INFO  @ Thu, 13 Apr 2017 18:53:01:  18000000 
INFO  @ Thu, 13 Apr 2017 18:53:02:  19000000 
INFO  @ Thu, 13 Apr 2017 18:53:04:  20000000 
INFO  @ Thu, 13 Apr 2017 18:53:05:  21000000 
INFO  @ Thu, 13 Apr 2017 18:53:07:  22000000 
INFO  @ Thu, 13 Apr 2017 18:53:08:  23000000 
INFO  @ Thu, 13 Apr 2017 18:53:10:  24000000 
INFO  @ Thu, 13 Apr 2017 18:53:12:  25000000 
INFO  @ Thu, 13 Apr 2017 18:53:13:  26000000 
INFO  @ Thu, 13 Apr 2017 18:53:15:  27000000 
INFO  @ Thu, 13 Apr 2017 18:53:16:  28000000 
INFO  @ Thu, 13 Apr 2017 18:53:18:  29000000 
INFO  @ Thu, 13 Apr 2017 18:53:20:  30000000 
INFO  @ Thu, 13 Apr 2017 18:53:21:  31000000 
INFO  @ Thu, 13 Apr 2017 18:53:23:  32000000 
INFO  @ Thu, 13 Apr 2017 18:53:24:  33000000 
INFO  @ Thu, 13 Apr 2017 18:53:26:  34000000 
INFO  @ Thu, 13 Apr 2017 18:53:28:  35000000 
INFO  @ Thu, 13 Apr 2017 18:53:29:  36000000 
INFO  @ Thu, 13 Apr 2017 18:53:31:  37000000 
INFO  @ Thu, 13 Apr 2017 18:53:32:  38000000 
INFO  @ Thu, 13 Apr 2017 18:53:34:  39000000 
INFO  @ Thu, 13 Apr 2017 18:53:36:  40000000 
INFO  @ Thu, 13 Apr 2017 18:53:37:  41000000 
INFO  @ Thu, 13 Apr 2017 18:53:39:  42000000 
INFO  @ Thu, 13 Apr 2017 18:53:41:  43000000 
INFO  @ Thu, 13 Apr 2017 18:53:42:  44000000 
INFO  @ Thu, 13 Apr 2017 18:53:44:  45000000 
INFO  @ Thu, 13 Apr 2017 18:53:46:  46000000 
INFO  @ Thu, 13 Apr 2017 18:53:47:  47000000 
INFO  @ Thu, 13 Apr 2017 18:53:49:  48000000 
INFO  @ Thu, 13 Apr 2017 18:53:50:  49000000 
INFO  @ Thu, 13 Apr 2017 18:53:52:  50000000 
INFO  @ Thu, 13 Apr 2017 18:53:54:  51000000 
INFO  @ Thu, 13 Apr 2017 18:53:55:  52000000 
INFO  @ Thu, 13 Apr 2017 18:53:57:  53000000 
INFO  @ Thu, 13 Apr 2017 18:53:58:  54000000 
INFO  @ Thu, 13 Apr 2017 18:54:00:  55000000 
INFO  @ Thu, 13 Apr 2017 18:54:02:  56000000 
INFO  @ Thu, 13 Apr 2017 18:54:03:  57000000 
INFO  @ Thu, 13 Apr 2017 18:54:05:  58000000 
INFO  @ Thu, 13 Apr 2017 18:54:07:  59000000 
INFO  @ Thu, 13 Apr 2017 18:54:08:  60000000 
INFO  @ Thu, 13 Apr 2017 18:54:10:  61000000 
INFO  @ Thu, 13 Apr 2017 18:54:11:  62000000 
INFO  @ Thu, 13 Apr 2017 18:54:13:  63000000 
INFO  @ Thu, 13 Apr 2017 18:54:18: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:54:20:  1000000 
INFO  @ Thu, 13 Apr 2017 18:54:22:  2000000 
INFO  @ Thu, 13 Apr 2017 18:54:23:  3000000 
INFO  @ Thu, 13 Apr 2017 18:54:24:  4000000 
INFO  @ Thu, 13 Apr 2017 18:54:26:  5000000 
INFO  @ Thu, 13 Apr 2017 18:54:27:  6000000 
INFO  @ Thu, 13 Apr 2017 18:54:29:  7000000 
INFO  @ Thu, 13 Apr 2017 18:54:30:  8000000 
INFO  @ Thu, 13 Apr 2017 18:54:32:  9000000 
INFO  @ Thu, 13 Apr 2017 18:54:33:  10000000 
INFO  @ Thu, 13 Apr 2017 18:54:35:  11000000 
INFO  @ Thu, 13 Apr 2017 18:54:36:  12000000 
INFO  @ Thu, 13 Apr 2017 18:54:38:  13000000 
INFO  @ Thu, 13 Apr 2017 18:54:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:54:41:  15000000 
INFO  @ Thu, 13 Apr 2017 18:54:42:  16000000 
INFO  @ Thu, 13 Apr 2017 18:54:44:  17000000 
INFO  @ Thu, 13 Apr 2017 18:54:45:  18000000 
INFO  @ Thu, 13 Apr 2017 18:54:46:  19000000 
INFO  @ Thu, 13 Apr 2017 18:54:48:  20000000 
INFO  @ Thu, 13 Apr 2017 18:54:50:  21000000 
INFO  @ Thu, 13 Apr 2017 18:54:51:  22000000 
INFO  @ Thu, 13 Apr 2017 18:54:52:  23000000 
INFO  @ Thu, 13 Apr 2017 18:54:54:  24000000 
INFO  @ Thu, 13 Apr 2017 18:54:55:  25000000 
INFO  @ Thu, 13 Apr 2017 18:54:57:  26000000 
INFO  @ Thu, 13 Apr 2017 18:54:58:  27000000 
INFO  @ Thu, 13 Apr 2017 18:55:00:  28000000 
INFO  @ Thu, 13 Apr 2017 18:55:01:  29000000 
INFO  @ Thu, 13 Apr 2017 18:55:03:  30000000 
INFO  @ Thu, 13 Apr 2017 18:55:04:  31000000 
INFO  @ Thu, 13 Apr 2017 18:55:06:  32000000 
INFO  @ Thu, 13 Apr 2017 18:55:07:  33000000 
INFO  @ Thu, 13 Apr 2017 18:55:09:  34000000 
INFO  @ Thu, 13 Apr 2017 18:55:10:  35000000 
INFO  @ Thu, 13 Apr 2017 18:55:12:  36000000 
INFO  @ Thu, 13 Apr 2017 18:55:13:  37000000 
INFO  @ Thu, 13 Apr 2017 18:55:15:  38000000 
INFO  @ Thu, 13 Apr 2017 18:55:17:  39000000 
INFO  @ Thu, 13 Apr 2017 18:55:18:  40000000 
INFO  @ Thu, 13 Apr 2017 18:55:19:  41000000 
INFO  @ Thu, 13 Apr 2017 18:55:21:  42000000 
INFO  @ Thu, 13 Apr 2017 18:55:22:  43000000 
INFO  @ Thu, 13 Apr 2017 18:55:24:  44000000 
INFO  @ Thu, 13 Apr 2017 18:55:25:  45000000 
INFO  @ Thu, 13 Apr 2017 18:55:27:  46000000 
INFO  @ Thu, 13 Apr 2017 18:55:28:  47000000 
INFO  @ Thu, 13 Apr 2017 18:55:30:  48000000 
INFO  @ Thu, 13 Apr 2017 18:55:31:  49000000 
INFO  @ Thu, 13 Apr 2017 18:55:33:  50000000 
INFO  @ Thu, 13 Apr 2017 18:55:34:  51000000 
INFO  @ Thu, 13 Apr 2017 18:55:36:  52000000 
INFO  @ Thu, 13 Apr 2017 18:55:37:  53000000 
INFO  @ Thu, 13 Apr 2017 18:55:39:  54000000 
INFO  @ Thu, 13 Apr 2017 18:55:40:  55000000 
INFO  @ Thu, 13 Apr 2017 18:55:42:  56000000 
INFO  @ Thu, 13 Apr 2017 18:55:43:  57000000 
INFO  @ Thu, 13 Apr 2017 18:55:45:  58000000 
INFO  @ Thu, 13 Apr 2017 18:55:46:  59000000 
INFO  @ Thu, 13 Apr 2017 18:55:47:  60000000 
INFO  @ Thu, 13 Apr 2017 18:55:49:  61000000 
INFO  @ Thu, 13 Apr 2017 18:55:50:  62000000 
INFO  @ Thu, 13 Apr 2017 18:55:52:  63000000 
INFO  @ Thu, 13 Apr 2017 18:55:53:  64000000 
INFO  @ Thu, 13 Apr 2017 18:55:55:  65000000 
INFO  @ Thu, 13 Apr 2017 18:55:56:  66000000 
INFO  @ Thu, 13 Apr 2017 18:55:58:  67000000 
INFO  @ Thu, 13 Apr 2017 18:55:59:  68000000 
INFO  @ Thu, 13 Apr 2017 18:56:01:  69000000 
INFO  @ Thu, 13 Apr 2017 18:56:03:  70000000 
INFO  @ Thu, 13 Apr 2017 18:56:04:  71000000 
INFO  @ Thu, 13 Apr 2017 18:56:06:  72000000 
INFO  @ Thu, 13 Apr 2017 18:56:07:  73000000 
INFO  @ Thu, 13 Apr 2017 18:56:09:  74000000 
INFO  @ Thu, 13 Apr 2017 18:56:10:  75000000 
INFO  @ Thu, 13 Apr 2017 18:56:11:  76000000 
INFO  @ Thu, 13 Apr 2017 18:56:13:  77000000 
INFO  @ Thu, 13 Apr 2017 18:56:14:  78000000 
INFO  @ Thu, 13 Apr 2017 18:56:16:  79000000 
INFO  @ Thu, 13 Apr 2017 18:56:17:  80000000 
INFO  @ Thu, 13 Apr 2017 18:56:18:  81000000 
INFO  @ Thu, 13 Apr 2017 18:56:20:  82000000 
INFO  @ Thu, 13 Apr 2017 18:56:21:  83000000 
INFO  @ Thu, 13 Apr 2017 18:56:23:  84000000 
INFO  @ Thu, 13 Apr 2017 18:56:24:  85000000 
INFO  @ Thu, 13 Apr 2017 18:56:26:  86000000 
INFO  @ Thu, 13 Apr 2017 18:56:27:  87000000 
INFO  @ Thu, 13 Apr 2017 18:56:29:  88000000 
INFO  @ Thu, 13 Apr 2017 18:56:30:  89000000 
INFO  @ Thu, 13 Apr 2017 18:56:32:  90000000 
INFO  @ Thu, 13 Apr 2017 18:56:33:  91000000 
INFO  @ Thu, 13 Apr 2017 18:56:35:  92000000 
INFO  @ Thu, 13 Apr 2017 18:56:36:  93000000 
INFO  @ Thu, 13 Apr 2017 18:56:38:  94000000 
INFO  @ Thu, 13 Apr 2017 18:56:39:  95000000 
INFO  @ Thu, 13 Apr 2017 18:56:41:  96000000 
INFO  @ Thu, 13 Apr 2017 18:56:42:  97000000 
INFO  @ Thu, 13 Apr 2017 18:56:44:  98000000 
INFO  @ Thu, 13 Apr 2017 18:56:45:  99000000 
INFO  @ Thu, 13 Apr 2017 18:56:47: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:56:47: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:56:47: #1  total tags in treatment: 63752772 
INFO  @ Thu, 13 Apr 2017 18:56:47: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:56:47: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:56:47: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:56:47: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:56:47: #2 Use 235 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:56:47: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:56:47: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:56:47: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:02:46: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:06:22: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:06:23: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:06:24: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF066ZSK.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:06:26: Done!

Num	7
ID	task.callpeak_macs2.macs2_g_b_rep2.line_155.id_16
Name	macs2 g/b rep2
Thread	thread_Root
PID	47022

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:54:24
End	2017-04-13 19:10:45
Elapsed	00:16:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
32358 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:54:46: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:54:46: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:54:46: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:54:48:  1000000 
INFO  @ Thu, 13 Apr 2017 18:54:49:  2000000 
INFO  @ Thu, 13 Apr 2017 18:54:51:  3000000 
INFO  @ Thu, 13 Apr 2017 18:54:52:  4000000 
INFO  @ Thu, 13 Apr 2017 18:54:54:  5000000 
INFO  @ Thu, 13 Apr 2017 18:54:55:  6000000 
INFO  @ Thu, 13 Apr 2017 18:54:57:  7000000 
INFO  @ Thu, 13 Apr 2017 18:54:59:  8000000 
INFO  @ Thu, 13 Apr 2017 18:55:00:  9000000 
INFO  @ Thu, 13 Apr 2017 18:55:02:  10000000 
INFO  @ Thu, 13 Apr 2017 18:55:03:  11000000 
INFO  @ Thu, 13 Apr 2017 18:55:05:  12000000 
INFO  @ Thu, 13 Apr 2017 18:55:06:  13000000 
INFO  @ Thu, 13 Apr 2017 18:55:08:  14000000 
INFO  @ Thu, 13 Apr 2017 18:55:09:  15000000 
INFO  @ Thu, 13 Apr 2017 18:55:11:  16000000 
INFO  @ Thu, 13 Apr 2017 18:55:13:  17000000 
INFO  @ Thu, 13 Apr 2017 18:55:14:  18000000 
INFO  @ Thu, 13 Apr 2017 18:55:16:  19000000 
INFO  @ Thu, 13 Apr 2017 18:55:17:  20000000 
INFO  @ Thu, 13 Apr 2017 18:55:19:  21000000 
INFO  @ Thu, 13 Apr 2017 18:55:20:  22000000 
INFO  @ Thu, 13 Apr 2017 18:55:22:  23000000 
INFO  @ Thu, 13 Apr 2017 18:55:23:  24000000 
INFO  @ Thu, 13 Apr 2017 18:55:25:  25000000 
INFO  @ Thu, 13 Apr 2017 18:55:27:  26000000 
INFO  @ Thu, 13 Apr 2017 18:55:28:  27000000 
INFO  @ Thu, 13 Apr 2017 18:55:30:  28000000 
INFO  @ Thu, 13 Apr 2017 18:55:31:  29000000 
INFO  @ Thu, 13 Apr 2017 18:55:33:  30000000 
INFO  @ Thu, 13 Apr 2017 18:55:34:  31000000 
INFO  @ Thu, 13 Apr 2017 18:55:36:  32000000 
INFO  @ Thu, 13 Apr 2017 18:55:37:  33000000 
INFO  @ Thu, 13 Apr 2017 18:55:39:  34000000 
INFO  @ Thu, 13 Apr 2017 18:55:40:  35000000 
INFO  @ Thu, 13 Apr 2017 18:55:42:  36000000 
INFO  @ Thu, 13 Apr 2017 18:55:43:  37000000 
INFO  @ Thu, 13 Apr 2017 18:55:45:  38000000 
INFO  @ Thu, 13 Apr 2017 18:55:47:  39000000 
INFO  @ Thu, 13 Apr 2017 18:55:48:  40000000 
INFO  @ Thu, 13 Apr 2017 18:55:50:  41000000 
INFO  @ Thu, 13 Apr 2017 18:55:51:  42000000 
INFO  @ Thu, 13 Apr 2017 18:55:53:  43000000 
INFO  @ Thu, 13 Apr 2017 18:55:54:  44000000 
INFO  @ Thu, 13 Apr 2017 18:55:56:  45000000 
INFO  @ Thu, 13 Apr 2017 18:55:57:  46000000 
INFO  @ Thu, 13 Apr 2017 18:55:59:  47000000 
INFO  @ Thu, 13 Apr 2017 18:56:00:  48000000 
INFO  @ Thu, 13 Apr 2017 18:56:02:  49000000 
INFO  @ Thu, 13 Apr 2017 18:56:03:  50000000 
INFO  @ Thu, 13 Apr 2017 18:56:05:  51000000 
INFO  @ Thu, 13 Apr 2017 18:56:07:  52000000 
INFO  @ Thu, 13 Apr 2017 18:56:08:  53000000 
INFO  @ Thu, 13 Apr 2017 18:56:10:  54000000 
INFO  @ Thu, 13 Apr 2017 18:56:11:  55000000 
INFO  @ Thu, 13 Apr 2017 18:56:13:  56000000 
INFO  @ Thu, 13 Apr 2017 18:56:14:  57000000 
INFO  @ Thu, 13 Apr 2017 18:56:16:  58000000 
INFO  @ Thu, 13 Apr 2017 18:56:17:  59000000 
INFO  @ Thu, 13 Apr 2017 18:56:19:  60000000 
INFO  @ Thu, 13 Apr 2017 18:56:20:  61000000 
INFO  @ Thu, 13 Apr 2017 18:56:22:  62000000 
INFO  @ Thu, 13 Apr 2017 18:56:24:  63000000 
INFO  @ Thu, 13 Apr 2017 18:56:25:  64000000 
INFO  @ Thu, 13 Apr 2017 18:56:27:  65000000 
INFO  @ Thu, 13 Apr 2017 18:56:28:  66000000 
INFO  @ Thu, 13 Apr 2017 18:56:30:  67000000 
INFO  @ Thu, 13 Apr 2017 18:56:31:  68000000 
INFO  @ Thu, 13 Apr 2017 18:56:33:  69000000 
INFO  @ Thu, 13 Apr 2017 18:56:34:  70000000 
INFO  @ Thu, 13 Apr 2017 18:56:36:  71000000 
INFO  @ Thu, 13 Apr 2017 18:56:37:  72000000 
INFO  @ Thu, 13 Apr 2017 18:56:39:  73000000 
INFO  @ Thu, 13 Apr 2017 18:56:41:  74000000 
INFO  @ Thu, 13 Apr 2017 18:56:42:  75000000 
INFO  @ Thu, 13 Apr 2017 18:56:44:  76000000 
INFO  @ Thu, 13 Apr 2017 18:56:45:  77000000 
INFO  @ Thu, 13 Apr 2017 18:56:47:  78000000 
INFO  @ Thu, 13 Apr 2017 18:56:48:  79000000 
INFO  @ Thu, 13 Apr 2017 18:56:50:  80000000 
INFO  @ Thu, 13 Apr 2017 18:56:51:  81000000 
INFO  @ Thu, 13 Apr 2017 18:56:53:  82000000 
INFO  @ Thu, 13 Apr 2017 18:56:54:  83000000 
INFO  @ Thu, 13 Apr 2017 18:56:56:  84000000 
INFO  @ Thu, 13 Apr 2017 18:56:58:  85000000 
INFO  @ Thu, 13 Apr 2017 18:56:59:  86000000 
INFO  @ Thu, 13 Apr 2017 18:57:01:  87000000 
INFO  @ Thu, 13 Apr 2017 18:57:02:  88000000 
INFO  @ Thu, 13 Apr 2017 18:57:04:  89000000 
INFO  @ Thu, 13 Apr 2017 18:57:05:  90000000 
INFO  @ Thu, 13 Apr 2017 18:57:07:  91000000 
INFO  @ Thu, 13 Apr 2017 18:57:08:  92000000 
INFO  @ Thu, 13 Apr 2017 18:57:15: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:57:17:  1000000 
INFO  @ Thu, 13 Apr 2017 18:57:18:  2000000 
INFO  @ Thu, 13 Apr 2017 18:57:19:  3000000 
INFO  @ Thu, 13 Apr 2017 18:57:21:  4000000 
INFO  @ Thu, 13 Apr 2017 18:57:22:  5000000 
INFO  @ Thu, 13 Apr 2017 18:57:24:  6000000 
INFO  @ Thu, 13 Apr 2017 18:57:25:  7000000 
INFO  @ Thu, 13 Apr 2017 18:57:26:  8000000 
INFO  @ Thu, 13 Apr 2017 18:57:28:  9000000 
INFO  @ Thu, 13 Apr 2017 18:57:29:  10000000 
INFO  @ Thu, 13 Apr 2017 18:57:31:  11000000 
INFO  @ Thu, 13 Apr 2017 18:57:32:  12000000 
INFO  @ Thu, 13 Apr 2017 18:57:34:  13000000 
INFO  @ Thu, 13 Apr 2017 18:57:35:  14000000 
INFO  @ Thu, 13 Apr 2017 18:57:36:  15000000 
INFO  @ Thu, 13 Apr 2017 18:57:38:  16000000 
INFO  @ Thu, 13 Apr 2017 18:57:39:  17000000 
INFO  @ Thu, 13 Apr 2017 18:57:41:  18000000 
INFO  @ Thu, 13 Apr 2017 18:57:42:  19000000 
INFO  @ Thu, 13 Apr 2017 18:57:44:  20000000 
INFO  @ Thu, 13 Apr 2017 18:57:45:  21000000 
INFO  @ Thu, 13 Apr 2017 18:57:46:  22000000 
INFO  @ Thu, 13 Apr 2017 18:57:48:  23000000 
INFO  @ Thu, 13 Apr 2017 18:57:49:  24000000 
INFO  @ Thu, 13 Apr 2017 18:57:51:  25000000 
INFO  @ Thu, 13 Apr 2017 18:57:52:  26000000 
INFO  @ Thu, 13 Apr 2017 18:57:54:  27000000 
INFO  @ Thu, 13 Apr 2017 18:57:55:  28000000 
INFO  @ Thu, 13 Apr 2017 18:57:56:  29000000 
INFO  @ Thu, 13 Apr 2017 18:57:58:  30000000 
INFO  @ Thu, 13 Apr 2017 18:57:59:  31000000 
INFO  @ Thu, 13 Apr 2017 18:58:01:  32000000 
INFO  @ Thu, 13 Apr 2017 18:58:02:  33000000 
INFO  @ Thu, 13 Apr 2017 18:58:03:  34000000 
INFO  @ Thu, 13 Apr 2017 18:58:05:  35000000 
INFO  @ Thu, 13 Apr 2017 18:58:06:  36000000 
INFO  @ Thu, 13 Apr 2017 18:58:08:  37000000 
INFO  @ Thu, 13 Apr 2017 18:58:09:  38000000 
INFO  @ Thu, 13 Apr 2017 18:58:11:  39000000 
INFO  @ Thu, 13 Apr 2017 18:58:12:  40000000 
INFO  @ Thu, 13 Apr 2017 18:58:14:  41000000 
INFO  @ Thu, 13 Apr 2017 18:58:15:  42000000 
INFO  @ Thu, 13 Apr 2017 18:58:16:  43000000 
INFO  @ Thu, 13 Apr 2017 18:58:18:  44000000 
INFO  @ Thu, 13 Apr 2017 18:58:19:  45000000 
INFO  @ Thu, 13 Apr 2017 18:58:21:  46000000 
INFO  @ Thu, 13 Apr 2017 18:58:22:  47000000 
INFO  @ Thu, 13 Apr 2017 18:58:24:  48000000 
INFO  @ Thu, 13 Apr 2017 18:58:25:  49000000 
INFO  @ Thu, 13 Apr 2017 18:58:26:  50000000 
INFO  @ Thu, 13 Apr 2017 18:58:28:  51000000 
INFO  @ Thu, 13 Apr 2017 18:58:29:  52000000 
INFO  @ Thu, 13 Apr 2017 18:58:31:  53000000 
INFO  @ Thu, 13 Apr 2017 18:58:32:  54000000 
INFO  @ Thu, 13 Apr 2017 18:58:34:  55000000 
INFO  @ Thu, 13 Apr 2017 18:58:35:  56000000 
INFO  @ Thu, 13 Apr 2017 18:58:36:  57000000 
INFO  @ Thu, 13 Apr 2017 18:58:38:  58000000 
INFO  @ Thu, 13 Apr 2017 18:58:39:  59000000 
INFO  @ Thu, 13 Apr 2017 18:58:41:  60000000 
INFO  @ Thu, 13 Apr 2017 18:58:42:  61000000 
INFO  @ Thu, 13 Apr 2017 18:58:44:  62000000 
INFO  @ Thu, 13 Apr 2017 18:58:45:  63000000 
INFO  @ Thu, 13 Apr 2017 18:58:46:  64000000 
INFO  @ Thu, 13 Apr 2017 18:58:48:  65000000 
INFO  @ Thu, 13 Apr 2017 18:58:49:  66000000 
INFO  @ Thu, 13 Apr 2017 18:58:51:  67000000 
INFO  @ Thu, 13 Apr 2017 18:58:52:  68000000 
INFO  @ Thu, 13 Apr 2017 18:58:54:  69000000 
INFO  @ Thu, 13 Apr 2017 18:58:55:  70000000 
INFO  @ Thu, 13 Apr 2017 18:58:56:  71000000 
INFO  @ Thu, 13 Apr 2017 18:58:58:  72000000 
INFO  @ Thu, 13 Apr 2017 18:58:59:  73000000 
INFO  @ Thu, 13 Apr 2017 18:59:01:  74000000 
INFO  @ Thu, 13 Apr 2017 18:59:02:  75000000 
INFO  @ Thu, 13 Apr 2017 18:59:04:  76000000 
INFO  @ Thu, 13 Apr 2017 18:59:05:  77000000 
INFO  @ Thu, 13 Apr 2017 18:59:07:  78000000 
INFO  @ Thu, 13 Apr 2017 18:59:08:  79000000 
INFO  @ Thu, 13 Apr 2017 18:59:09:  80000000 
INFO  @ Thu, 13 Apr 2017 18:59:11:  81000000 
INFO  @ Thu, 13 Apr 2017 18:59:12:  82000000 
INFO  @ Thu, 13 Apr 2017 18:59:14:  83000000 
INFO  @ Thu, 13 Apr 2017 18:59:15:  84000000 
INFO  @ Thu, 13 Apr 2017 18:59:17:  85000000 
INFO  @ Thu, 13 Apr 2017 18:59:18:  86000000 
INFO  @ Thu, 13 Apr 2017 18:59:19:  87000000 
INFO  @ Thu, 13 Apr 2017 18:59:21:  88000000 
INFO  @ Thu, 13 Apr 2017 18:59:22:  89000000 
INFO  @ Thu, 13 Apr 2017 18:59:24:  90000000 
INFO  @ Thu, 13 Apr 2017 18:59:25:  91000000 
INFO  @ Thu, 13 Apr 2017 18:59:27:  92000000 
INFO  @ Thu, 13 Apr 2017 18:59:28:  93000000 
INFO  @ Thu, 13 Apr 2017 18:59:29:  94000000 
INFO  @ Thu, 13 Apr 2017 18:59:31:  95000000 
INFO  @ Thu, 13 Apr 2017 18:59:32:  96000000 
INFO  @ Thu, 13 Apr 2017 18:59:34:  97000000 
INFO  @ Thu, 13 Apr 2017 18:59:35:  98000000 
INFO  @ Thu, 13 Apr 2017 18:59:36:  99000000 
INFO  @ Thu, 13 Apr 2017 18:59:38: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:59:38: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:59:38: #1  total tags in treatment: 92229774 
INFO  @ Thu, 13 Apr 2017 18:59:38: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:59:38: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:59:38: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:59:38: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:59:38: #2 Use 240 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:59:38: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:59:38: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:59:38: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:06:57: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:10:41: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:10:41: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:10:42: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:10:42: Done!

Num	8
ID	task.callpeak_macs2.macs2_g_b_rep2_pr1.line_155.id_17
Name	macs2 g/b rep2-pr1
Thread	thread_Root
PID	47023

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:54:45
End	2017-04-13 19:14:58
Elapsed	00:20:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
20534 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:55:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:55:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:55:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:55:04:  1000000 
INFO  @ Thu, 13 Apr 2017 18:55:06:  2000000 
INFO  @ Thu, 13 Apr 2017 18:55:08:  3000000 
INFO  @ Thu, 13 Apr 2017 18:55:11:  4000000 
INFO  @ Thu, 13 Apr 2017 18:55:13:  5000000 
INFO  @ Thu, 13 Apr 2017 18:55:15:  6000000 
INFO  @ Thu, 13 Apr 2017 18:55:17:  7000000 
INFO  @ Thu, 13 Apr 2017 18:55:19:  8000000 
INFO  @ Thu, 13 Apr 2017 18:55:21:  9000000 
INFO  @ Thu, 13 Apr 2017 18:55:23:  10000000 
INFO  @ Thu, 13 Apr 2017 18:55:25:  11000000 
INFO  @ Thu, 13 Apr 2017 18:55:27:  12000000 
INFO  @ Thu, 13 Apr 2017 18:55:29:  13000000 
INFO  @ Thu, 13 Apr 2017 18:55:31:  14000000 
INFO  @ Thu, 13 Apr 2017 18:55:33:  15000000 
INFO  @ Thu, 13 Apr 2017 18:55:35:  16000000 
INFO  @ Thu, 13 Apr 2017 18:55:37:  17000000 
INFO  @ Thu, 13 Apr 2017 18:55:39:  18000000 
INFO  @ Thu, 13 Apr 2017 18:55:41:  19000000 
INFO  @ Thu, 13 Apr 2017 18:55:43:  20000000 
INFO  @ Thu, 13 Apr 2017 18:55:45:  21000000 
INFO  @ Thu, 13 Apr 2017 18:55:47:  22000000 
INFO  @ Thu, 13 Apr 2017 18:55:48:  23000000 
INFO  @ Thu, 13 Apr 2017 18:55:50:  24000000 
INFO  @ Thu, 13 Apr 2017 18:55:52:  25000000 
INFO  @ Thu, 13 Apr 2017 18:55:54:  26000000 
INFO  @ Thu, 13 Apr 2017 18:55:56:  27000000 
INFO  @ Thu, 13 Apr 2017 18:55:58:  28000000 
INFO  @ Thu, 13 Apr 2017 18:56:00:  29000000 
INFO  @ Thu, 13 Apr 2017 18:56:02:  30000000 
INFO  @ Thu, 13 Apr 2017 18:56:04:  31000000 
INFO  @ Thu, 13 Apr 2017 18:56:06:  32000000 
INFO  @ Thu, 13 Apr 2017 18:56:08:  33000000 
INFO  @ Thu, 13 Apr 2017 18:56:10:  34000000 
INFO  @ Thu, 13 Apr 2017 18:56:12:  35000000 
INFO  @ Thu, 13 Apr 2017 18:56:14:  36000000 
INFO  @ Thu, 13 Apr 2017 18:56:16:  37000000 
INFO  @ Thu, 13 Apr 2017 18:56:18:  38000000 
INFO  @ Thu, 13 Apr 2017 18:56:20:  39000000 
INFO  @ Thu, 13 Apr 2017 18:56:22:  40000000 
INFO  @ Thu, 13 Apr 2017 18:56:24:  41000000 
INFO  @ Thu, 13 Apr 2017 18:56:26:  42000000 
INFO  @ Thu, 13 Apr 2017 18:56:28:  43000000 
INFO  @ Thu, 13 Apr 2017 18:56:30:  44000000 
INFO  @ Thu, 13 Apr 2017 18:56:32:  45000000 
INFO  @ Thu, 13 Apr 2017 18:56:34:  46000000 
INFO  @ Thu, 13 Apr 2017 18:56:38: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:56:40:  1000000 
INFO  @ Thu, 13 Apr 2017 18:56:42:  2000000 
INFO  @ Thu, 13 Apr 2017 18:56:44:  3000000 
INFO  @ Thu, 13 Apr 2017 18:56:46:  4000000 
INFO  @ Thu, 13 Apr 2017 18:56:48:  5000000 
INFO  @ Thu, 13 Apr 2017 18:56:50:  6000000 
INFO  @ Thu, 13 Apr 2017 18:56:52:  7000000 
INFO  @ Thu, 13 Apr 2017 18:56:53:  8000000 
INFO  @ Thu, 13 Apr 2017 18:56:55:  9000000 
INFO  @ Thu, 13 Apr 2017 18:56:57:  10000000 
INFO  @ Thu, 13 Apr 2017 18:56:59:  11000000 
INFO  @ Thu, 13 Apr 2017 18:57:01:  12000000 
INFO  @ Thu, 13 Apr 2017 18:57:02:  13000000 
INFO  @ Thu, 13 Apr 2017 18:57:04:  14000000 
INFO  @ Thu, 13 Apr 2017 18:57:06:  15000000 
INFO  @ Thu, 13 Apr 2017 18:57:08:  16000000 
INFO  @ Thu, 13 Apr 2017 18:57:10:  17000000 
INFO  @ Thu, 13 Apr 2017 18:57:12:  18000000 
INFO  @ Thu, 13 Apr 2017 18:57:14:  19000000 
INFO  @ Thu, 13 Apr 2017 18:57:15:  20000000 
INFO  @ Thu, 13 Apr 2017 18:57:17:  21000000 
INFO  @ Thu, 13 Apr 2017 18:57:19:  22000000 
INFO  @ Thu, 13 Apr 2017 18:57:21:  23000000 
INFO  @ Thu, 13 Apr 2017 18:57:23:  24000000 
INFO  @ Thu, 13 Apr 2017 18:57:25:  25000000 
INFO  @ Thu, 13 Apr 2017 18:57:27:  26000000 
INFO  @ Thu, 13 Apr 2017 18:57:28:  27000000 
INFO  @ Thu, 13 Apr 2017 18:57:30:  28000000 
INFO  @ Thu, 13 Apr 2017 18:57:32:  29000000 
INFO  @ Thu, 13 Apr 2017 18:57:34:  30000000 
INFO  @ Thu, 13 Apr 2017 18:57:36:  31000000 
INFO  @ Thu, 13 Apr 2017 18:57:37:  32000000 
INFO  @ Thu, 13 Apr 2017 18:57:39:  33000000 
INFO  @ Thu, 13 Apr 2017 18:57:41:  34000000 
INFO  @ Thu, 13 Apr 2017 18:57:43:  35000000 
INFO  @ Thu, 13 Apr 2017 18:57:45:  36000000 
INFO  @ Thu, 13 Apr 2017 18:57:47:  37000000 
INFO  @ Thu, 13 Apr 2017 18:57:48:  38000000 
INFO  @ Thu, 13 Apr 2017 18:57:50:  39000000 
INFO  @ Thu, 13 Apr 2017 18:57:52:  40000000 
INFO  @ Thu, 13 Apr 2017 18:57:54:  41000000 
INFO  @ Thu, 13 Apr 2017 18:57:56:  42000000 
INFO  @ Thu, 13 Apr 2017 18:57:57:  43000000 
INFO  @ Thu, 13 Apr 2017 18:57:59:  44000000 
INFO  @ Thu, 13 Apr 2017 18:58:01:  45000000 
INFO  @ Thu, 13 Apr 2017 18:58:03:  46000000 
INFO  @ Thu, 13 Apr 2017 18:58:05:  47000000 
INFO  @ Thu, 13 Apr 2017 18:58:07:  48000000 
INFO  @ Thu, 13 Apr 2017 18:58:08:  49000000 
INFO  @ Thu, 13 Apr 2017 18:58:10:  50000000 
INFO  @ Thu, 13 Apr 2017 18:58:12:  51000000 
INFO  @ Thu, 13 Apr 2017 18:58:14:  52000000 
INFO  @ Thu, 13 Apr 2017 18:58:16:  53000000 
INFO  @ Thu, 13 Apr 2017 18:58:18:  54000000 
INFO  @ Thu, 13 Apr 2017 18:58:19:  55000000 
INFO  @ Thu, 13 Apr 2017 18:58:21:  56000000 
INFO  @ Thu, 13 Apr 2017 18:58:23:  57000000 
INFO  @ Thu, 13 Apr 2017 18:58:25:  58000000 
INFO  @ Thu, 13 Apr 2017 18:58:27:  59000000 
INFO  @ Thu, 13 Apr 2017 18:58:28:  60000000 
INFO  @ Thu, 13 Apr 2017 18:58:30:  61000000 
INFO  @ Thu, 13 Apr 2017 18:58:32:  62000000 
INFO  @ Thu, 13 Apr 2017 18:58:34:  63000000 
INFO  @ Thu, 13 Apr 2017 18:58:36:  64000000 
INFO  @ Thu, 13 Apr 2017 18:58:38:  65000000 
INFO  @ Thu, 13 Apr 2017 18:58:40:  66000000 
INFO  @ Thu, 13 Apr 2017 18:58:42:  67000000 
INFO  @ Thu, 13 Apr 2017 18:58:43:  68000000 
INFO  @ Thu, 13 Apr 2017 18:58:45:  69000000 
INFO  @ Thu, 13 Apr 2017 18:58:47:  70000000 
INFO  @ Thu, 13 Apr 2017 18:58:49:  71000000 
INFO  @ Thu, 13 Apr 2017 18:58:51:  72000000 
INFO  @ Thu, 13 Apr 2017 18:58:52:  73000000 
INFO  @ Thu, 13 Apr 2017 18:58:54:  74000000 
INFO  @ Thu, 13 Apr 2017 18:58:56:  75000000 
INFO  @ Thu, 13 Apr 2017 18:58:58:  76000000 
INFO  @ Thu, 13 Apr 2017 18:59:00:  77000000 
INFO  @ Thu, 13 Apr 2017 18:59:02:  78000000 
INFO  @ Thu, 13 Apr 2017 18:59:03:  79000000 
INFO  @ Thu, 13 Apr 2017 18:59:05:  80000000 
INFO  @ Thu, 13 Apr 2017 18:59:07:  81000000 
INFO  @ Thu, 13 Apr 2017 18:59:09:  82000000 
INFO  @ Thu, 13 Apr 2017 18:59:11:  83000000 
INFO  @ Thu, 13 Apr 2017 18:59:13:  84000000 
INFO  @ Thu, 13 Apr 2017 18:59:14:  85000000 
INFO  @ Thu, 13 Apr 2017 18:59:16:  86000000 
INFO  @ Thu, 13 Apr 2017 18:59:18:  87000000 
INFO  @ Thu, 13 Apr 2017 18:59:20:  88000000 
INFO  @ Thu, 13 Apr 2017 18:59:22:  89000000 
INFO  @ Thu, 13 Apr 2017 18:59:24:  90000000 
INFO  @ Thu, 13 Apr 2017 18:59:25:  91000000 
INFO  @ Thu, 13 Apr 2017 18:59:27:  92000000 
INFO  @ Thu, 13 Apr 2017 18:59:29:  93000000 
INFO  @ Thu, 13 Apr 2017 18:59:31:  94000000 
INFO  @ Thu, 13 Apr 2017 18:59:33:  95000000 
INFO  @ Thu, 13 Apr 2017 18:59:35:  96000000 
INFO  @ Thu, 13 Apr 2017 18:59:37:  97000000 
INFO  @ Thu, 13 Apr 2017 18:59:38:  98000000 
INFO  @ Thu, 13 Apr 2017 18:59:40:  99000000 
INFO  @ Thu, 13 Apr 2017 18:59:42: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:59:42: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:59:42: #1  total tags in treatment: 46114888 
INFO  @ Thu, 13 Apr 2017 18:59:42: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:59:42: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:59:42: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:59:42: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:59:42: #2 Use 240 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:59:42: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:59:42: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:59:42: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:09:09: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:14:50: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:14:51: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:14:52: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:14:53: Done!

Num	9
ID	task.callpeak_macs2.macs2_g_b_rep2_pr2.line_155.id_18
Name	macs2 g/b rep2-pr2
Thread	thread_Root
PID	47025

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 18:57:08
End	2017-04-13 19:09:49
Elapsed	00:12:41
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Dependencies

 
# SYS command. line 157

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 158

 export LC_COLLATE=C

# SYS command. line 163

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz

# SYS command. line 167

 sort -k 14gr,14gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 175

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
38589 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:57:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz -c /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -f BED -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 240 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:57:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:57:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:57:33:  1000000 
INFO  @ Thu, 13 Apr 2017 18:57:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:57:36:  3000000 
INFO  @ Thu, 13 Apr 2017 18:57:38:  4000000 
INFO  @ Thu, 13 Apr 2017 18:57:39:  5000000 
INFO  @ Thu, 13 Apr 2017 18:57:41:  6000000 
INFO  @ Thu, 13 Apr 2017 18:57:42:  7000000 
INFO  @ Thu, 13 Apr 2017 18:57:44:  8000000 
INFO  @ Thu, 13 Apr 2017 18:57:45:  9000000 
INFO  @ Thu, 13 Apr 2017 18:57:47:  10000000 
INFO  @ Thu, 13 Apr 2017 18:57:49:  11000000 
INFO  @ Thu, 13 Apr 2017 18:57:50:  12000000 
INFO  @ Thu, 13 Apr 2017 18:57:52:  13000000 
INFO  @ Thu, 13 Apr 2017 18:57:53:  14000000 
INFO  @ Thu, 13 Apr 2017 18:57:55:  15000000 
INFO  @ Thu, 13 Apr 2017 18:57:56:  16000000 
INFO  @ Thu, 13 Apr 2017 18:57:58:  17000000 
INFO  @ Thu, 13 Apr 2017 18:58:00:  18000000 
INFO  @ Thu, 13 Apr 2017 18:58:01:  19000000 
INFO  @ Thu, 13 Apr 2017 18:58:03:  20000000 
INFO  @ Thu, 13 Apr 2017 18:58:05:  21000000 
INFO  @ Thu, 13 Apr 2017 18:58:06:  22000000 
INFO  @ Thu, 13 Apr 2017 18:58:08:  23000000 
INFO  @ Thu, 13 Apr 2017 18:58:09:  24000000 
INFO  @ Thu, 13 Apr 2017 18:58:11:  25000000 
INFO  @ Thu, 13 Apr 2017 18:58:13:  26000000 
INFO  @ Thu, 13 Apr 2017 18:58:14:  27000000 
INFO  @ Thu, 13 Apr 2017 18:58:16:  28000000 
INFO  @ Thu, 13 Apr 2017 18:58:17:  29000000 
INFO  @ Thu, 13 Apr 2017 18:58:19:  30000000 
INFO  @ Thu, 13 Apr 2017 18:58:20:  31000000 
INFO  @ Thu, 13 Apr 2017 18:58:22:  32000000 
INFO  @ Thu, 13 Apr 2017 18:58:23:  33000000 
INFO  @ Thu, 13 Apr 2017 18:58:25:  34000000 
INFO  @ Thu, 13 Apr 2017 18:58:26:  35000000 
INFO  @ Thu, 13 Apr 2017 18:58:28:  36000000 
INFO  @ Thu, 13 Apr 2017 18:58:29:  37000000 
INFO  @ Thu, 13 Apr 2017 18:58:31:  38000000 
INFO  @ Thu, 13 Apr 2017 18:58:32:  39000000 
INFO  @ Thu, 13 Apr 2017 18:58:34:  40000000 
INFO  @ Thu, 13 Apr 2017 18:58:36:  41000000 
INFO  @ Thu, 13 Apr 2017 18:58:37:  42000000 
INFO  @ Thu, 13 Apr 2017 18:58:39:  43000000 
INFO  @ Thu, 13 Apr 2017 18:58:40:  44000000 
INFO  @ Thu, 13 Apr 2017 18:58:42:  45000000 
INFO  @ Thu, 13 Apr 2017 18:58:43:  46000000 
INFO  @ Thu, 13 Apr 2017 18:58:47: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:58:48:  1000000 
INFO  @ Thu, 13 Apr 2017 18:58:49:  2000000 
INFO  @ Thu, 13 Apr 2017 18:58:51:  3000000 
INFO  @ Thu, 13 Apr 2017 18:58:52:  4000000 
INFO  @ Thu, 13 Apr 2017 18:58:54:  5000000 
INFO  @ Thu, 13 Apr 2017 18:58:55:  6000000 
INFO  @ Thu, 13 Apr 2017 18:58:56:  7000000 
INFO  @ Thu, 13 Apr 2017 18:58:58:  8000000 
INFO  @ Thu, 13 Apr 2017 18:58:59:  9000000 
INFO  @ Thu, 13 Apr 2017 18:59:00:  10000000 
INFO  @ Thu, 13 Apr 2017 18:59:02:  11000000 
INFO  @ Thu, 13 Apr 2017 18:59:03:  12000000 
INFO  @ Thu, 13 Apr 2017 18:59:05:  13000000 
INFO  @ Thu, 13 Apr 2017 18:59:06:  14000000 
INFO  @ Thu, 13 Apr 2017 18:59:07:  15000000 
INFO  @ Thu, 13 Apr 2017 18:59:09:  16000000 
INFO  @ Thu, 13 Apr 2017 18:59:10:  17000000 
INFO  @ Thu, 13 Apr 2017 18:59:12:  18000000 
INFO  @ Thu, 13 Apr 2017 18:59:13:  19000000 
INFO  @ Thu, 13 Apr 2017 18:59:14:  20000000 
INFO  @ Thu, 13 Apr 2017 18:59:16:  21000000 
INFO  @ Thu, 13 Apr 2017 18:59:17:  22000000 
INFO  @ Thu, 13 Apr 2017 18:59:19:  23000000 
INFO  @ Thu, 13 Apr 2017 18:59:20:  24000000 
INFO  @ Thu, 13 Apr 2017 18:59:21:  25000000 
INFO  @ Thu, 13 Apr 2017 18:59:23:  26000000 
INFO  @ Thu, 13 Apr 2017 18:59:24:  27000000 
INFO  @ Thu, 13 Apr 2017 18:59:26:  28000000 
INFO  @ Thu, 13 Apr 2017 18:59:27:  29000000 
INFO  @ Thu, 13 Apr 2017 18:59:28:  30000000 
INFO  @ Thu, 13 Apr 2017 18:59:30:  31000000 
INFO  @ Thu, 13 Apr 2017 18:59:31:  32000000 
INFO  @ Thu, 13 Apr 2017 18:59:33:  33000000 
INFO  @ Thu, 13 Apr 2017 18:59:34:  34000000 
INFO  @ Thu, 13 Apr 2017 18:59:35:  35000000 
INFO  @ Thu, 13 Apr 2017 18:59:37:  36000000 
INFO  @ Thu, 13 Apr 2017 18:59:38:  37000000 
INFO  @ Thu, 13 Apr 2017 18:59:39:  38000000 
INFO  @ Thu, 13 Apr 2017 18:59:41:  39000000 
INFO  @ Thu, 13 Apr 2017 18:59:42:  40000000 
INFO  @ Thu, 13 Apr 2017 18:59:44:  41000000 
INFO  @ Thu, 13 Apr 2017 18:59:45:  42000000 
INFO  @ Thu, 13 Apr 2017 18:59:46:  43000000 
INFO  @ Thu, 13 Apr 2017 18:59:48:  44000000 
INFO  @ Thu, 13 Apr 2017 18:59:49:  45000000 
INFO  @ Thu, 13 Apr 2017 18:59:51:  46000000 
INFO  @ Thu, 13 Apr 2017 18:59:52:  47000000 
INFO  @ Thu, 13 Apr 2017 18:59:53:  48000000 
INFO  @ Thu, 13 Apr 2017 18:59:55:  49000000 
INFO  @ Thu, 13 Apr 2017 18:59:56:  50000000 
INFO  @ Thu, 13 Apr 2017 18:59:58:  51000000 
INFO  @ Thu, 13 Apr 2017 18:59:59:  52000000 
INFO  @ Thu, 13 Apr 2017 19:00:00:  53000000 
INFO  @ Thu, 13 Apr 2017 19:00:02:  54000000 
INFO  @ Thu, 13 Apr 2017 19:00:03:  55000000 
INFO  @ Thu, 13 Apr 2017 19:00:04:  56000000 
INFO  @ Thu, 13 Apr 2017 19:00:06:  57000000 
INFO  @ Thu, 13 Apr 2017 19:00:07:  58000000 
INFO  @ Thu, 13 Apr 2017 19:00:09:  59000000 
INFO  @ Thu, 13 Apr 2017 19:00:10:  60000000 
INFO  @ Thu, 13 Apr 2017 19:00:11:  61000000 
INFO  @ Thu, 13 Apr 2017 19:00:13:  62000000 
INFO  @ Thu, 13 Apr 2017 19:00:14:  63000000 
INFO  @ Thu, 13 Apr 2017 19:00:16:  64000000 
INFO  @ Thu, 13 Apr 2017 19:00:17:  65000000 
INFO  @ Thu, 13 Apr 2017 19:00:18:  66000000 
INFO  @ Thu, 13 Apr 2017 19:00:20:  67000000 
INFO  @ Thu, 13 Apr 2017 19:00:21:  68000000 
INFO  @ Thu, 13 Apr 2017 19:00:23:  69000000 
INFO  @ Thu, 13 Apr 2017 19:00:24:  70000000 
INFO  @ Thu, 13 Apr 2017 19:00:25:  71000000 
INFO  @ Thu, 13 Apr 2017 19:00:27:  72000000 
INFO  @ Thu, 13 Apr 2017 19:00:28:  73000000 
INFO  @ Thu, 13 Apr 2017 19:00:30:  74000000 
INFO  @ Thu, 13 Apr 2017 19:00:31:  75000000 
INFO  @ Thu, 13 Apr 2017 19:00:32:  76000000 
INFO  @ Thu, 13 Apr 2017 19:00:34:  77000000 
INFO  @ Thu, 13 Apr 2017 19:00:35:  78000000 
INFO  @ Thu, 13 Apr 2017 19:00:37:  79000000 
INFO  @ Thu, 13 Apr 2017 19:00:38:  80000000 
INFO  @ Thu, 13 Apr 2017 19:00:39:  81000000 
INFO  @ Thu, 13 Apr 2017 19:00:41:  82000000 
INFO  @ Thu, 13 Apr 2017 19:00:42:  83000000 
INFO  @ Thu, 13 Apr 2017 19:00:43:  84000000 
INFO  @ Thu, 13 Apr 2017 19:00:45:  85000000 
INFO  @ Thu, 13 Apr 2017 19:00:46:  86000000 
INFO  @ Thu, 13 Apr 2017 19:00:48:  87000000 
INFO  @ Thu, 13 Apr 2017 19:00:49:  88000000 
INFO  @ Thu, 13 Apr 2017 19:00:50:  89000000 
INFO  @ Thu, 13 Apr 2017 19:00:52:  90000000 
INFO  @ Thu, 13 Apr 2017 19:00:53:  91000000 
INFO  @ Thu, 13 Apr 2017 19:00:55:  92000000 
INFO  @ Thu, 13 Apr 2017 19:00:56:  93000000 
INFO  @ Thu, 13 Apr 2017 19:00:57:  94000000 
INFO  @ Thu, 13 Apr 2017 19:00:59:  95000000 
INFO  @ Thu, 13 Apr 2017 19:01:00:  96000000 
INFO  @ Thu, 13 Apr 2017 19:01:01:  97000000 
INFO  @ Thu, 13 Apr 2017 19:01:03:  98000000 
INFO  @ Thu, 13 Apr 2017 19:01:04:  99000000 
INFO  @ Thu, 13 Apr 2017 19:01:06: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 19:01:06: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 19:01:06: #1  total tags in treatment: 46114886 
INFO  @ Thu, 13 Apr 2017 19:01:06: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 19:01:06: #1 finished! 
INFO  @ Thu, 13 Apr 2017 19:01:06: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 19:01:06: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 19:01:06: #2 Use 240 as fragment length 
INFO  @ Thu, 13 Apr 2017 19:01:06: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 19:01:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 19:01:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:06:25: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:09:43: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:09:44: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:09:45: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:09:45: Done!

Num	10
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_19
Name	naive_overlap
Thread	thread_Root
PID	47033

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 19:15:00
End	2017-04-13 19:16:15
Elapsed	00:01:15
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Dependencies

 
# SYS command. line 145

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) |    awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.gappedPeak.gz

# SYS command. line 156

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.gappedPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
28203 (process ID) old priority 0, new priority 19
Waiting for 58 seconds.

Num	11
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_20
Name	naive_overlap
Thread	thread_Root
PID	47034

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 19:15:02
End	2017-04-13 19:16:14
Elapsed	00:01:12
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
Dependencies

 
# SYS command. line 145

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 148

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep1/ENCFF066ZSK.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/rep2/ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz

# SYS command. line 151

 intersectBed  -wo -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_rep/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF066ZSK.pr1_ENCFF241VRG.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) | awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | intersectBed  -wo -a stdin -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF066ZSK.pr2_ENCFF241VRG.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) |    awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$12-$11; if (($19/s1 >= 0.5) || ($19/s2 >= 0.5)) {print $0}}' | cut -f 1-9 | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.broadPeak.gz

# SYS command. line 156

 bedtools intersect -v -a <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.broadPeak.gz) -b <(zcat -f /mnt/data/bds_pipeline_genome_data/hg38_ENCODE/hg38.blacklist.bed.gz)  | grep -P 'chr[\dXY]+[ \t]' | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.broadPeak.gz

# SYS command. line 158

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 160

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi

   
--------------------Stdout--------------------
28202 (process ID) old priority 0, new priority 19
Waiting for 58 seconds.

Num	12
ID	task.report.peak2hammock.line_361.id_23
Name	peak2hammock
Thread	thread_Root
PID	31339

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 19:16:20
End	2017-04-13 19:16:29
Elapsed	00:00:09
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock.gz
Dependencies

 
# SYS command. line 363

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 364

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

# SYS command. line 366

 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils/gappedpeak.py /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.hammock

# SYS command. line 367

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/peak/macs2/overlap/ENCFF066ZSK_ENCFF241VRG.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
31344 (process ID) old priority 0, new priority 19

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	31815

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus
Mem

Start	2017-04-13 19:16:30
End	2017-04-13 19:16:39
Elapsed	00:00:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 98

 if [[ -f $(which /software/miniconda3/bin/conda) && $(/software/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /software/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); if (( $(nice)<19 )); then renice -n 19 $$; fi

# SYS command. line 99

 dot -Tsvg /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/report/ZBTB26_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
31819 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, ZBTB26_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB26_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep1/ENCFF066ZSK.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2/out/align/rep2/ENCFF241VRG.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -histone, $]
bool	canFail	false
string	CPATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int	cpus	-1
int	cpusLocal	56
int	day	86400
string	DEEPLIFT_DIR	/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string	DERBY_HOME	/usr/lib/jvm/java-8-oracle/db
string	DISPLAY	localhost:12.0
real	E	2.718281828459045
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string	EVENT_NOEPOLL	1
int	G	1073741824
string	HOME	/users/imk1/
int	hour	3600
string	J2REDIR	/usr/lib/jvm/java-8-oracle/jre
string	J2SDKDIR	/usr/lib/jvm/java-8-oracle
string	JAVA_HOME	/usr/lib/jvm/java-8-oracle
int	K	1024
string	KERAS_DIR	/users/imk1/.local/lib/python2.7/site-packages/keras/
string	KRB5CCNAME	FILE:/tmp/krb5cc_1048_CCx82k
string	LANG	en_US.UTF-8
string	LIBRARY_PATH	/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string	LOADEDMODULES
string	LOGNAME	imk1
int	M	1048576
string	MAIL	/var/mail/imk1
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/anaconda2/bin:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/scratch/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:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/users/imk1/edirect:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts//exec:/users/imk1/edirect:/snap/bin:/software/miniconda3/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/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/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2
string	programName	chipseq.bds
string	programPath	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
string	PWD	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB26_MACS2
string	PYTHONPATH	/users/imk1/.local/lib/python2.7/site-packages/keras/:/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	4
string	SSH_CLIENT	171.65.77.8 57066 22
string	SSH_CONNECTION	171.65.77.8 57067 171.65.76.63 22
string	SSH_TTY	/dev/pts/4
string	STY	46169.ZBTB26_MACS2.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	TMUX	/tmp/tmux-1048/default,43619,2
string	TMUX_PANE	%2
string	USER	imk1
string	UTIL_SCRIPTS_DIR	/srv/scratch/shared/surya/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	67062
string	XFILESEARCHPATH	/usr/dt/app-defaults/%L/Dt

BigDataScript report: chipseq.bds

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Parallel (threads) details

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