Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_183732_498
Start time	2017-04-13 18:37:32
Run time	00:37:40.905
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, EGR2_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/EGR2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.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_183732_498/task.callpeak_macs2.macs2_g_b_pooled_rep.line_155.id_10 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_ppr1.line_155.id_11 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_ppr2.line_155.id_12 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_rep1.line_155.id_13 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_14 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_15 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_rep2.line_155.id_16 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_rep2_pr1.line_155.id_17 chipseq.bds.20170413_183732_498/task.callpeak_macs2.macs2_g_b_rep2_pr2.line_155.id_18 chipseq.bds.20170413_183732_498/task.callpeak_naive_overlap.naive_overlap.line_143.id_19 chipseq.bds.20170413_183732_498/task.callpeak_naive_overlap.naive_overlap.line_143.id_20 chipseq.bds.20170413_183732_498/task.report.peak2hammock.line_361.id_23 chipseq.bds.20170413_183732_498/task.graphviz.report.line_97.id_24
thread_41	thread_Root
thread_42	thread_Root
thread_43	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	46963

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

Start	2017-04-13 18:37:45
End	2017-04-13 18:59:48
Elapsed	00:22:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 210 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.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--------------------
13997 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 210 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_rep/ENCFF888DOH_ENCFF234ALA.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 18:38:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:04:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:06:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:08:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:10:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:12:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:14:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:16:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:19:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  25000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  26000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  27000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  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 18:39:37: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:39:39:  1000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  2000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  3000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  4000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  5000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  6000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  7000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  12000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  13000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  14000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  15000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  16000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  17000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  18000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  19000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  20000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  21000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  22000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  23000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  24000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  25000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  26000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  27000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  28000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  29000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  30000000 
INFO  @ Thu, 13 Apr 2017 18:40:34:  31000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  32000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  33000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  34000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  35000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  36000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  37000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  38000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  39000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  40000000 
INFO  @ Thu, 13 Apr 2017 18:40:53:  41000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  42000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  44000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  45000000 
INFO  @ Thu, 13 Apr 2017 18:41:02:  46000000 
INFO  @ Thu, 13 Apr 2017 18:41:04:  47000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  48000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  49000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  50000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  51000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  52000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  53000000 
INFO  @ Thu, 13 Apr 2017 18:41:17:  54000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  55000000 
INFO  @ Thu, 13 Apr 2017 18:41:21:  56000000 
INFO  @ Thu, 13 Apr 2017 18:41:23:  57000000 
INFO  @ Thu, 13 Apr 2017 18:41:24:  58000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  59000000 
INFO  @ Thu, 13 Apr 2017 18:41:28:  60000000 
INFO  @ Thu, 13 Apr 2017 18:41:30:  61000000 
INFO  @ Thu, 13 Apr 2017 18:41:32:  62000000 
INFO  @ Thu, 13 Apr 2017 18:41:34:  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 18:41:43:  68000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  69000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  70000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  71000000 
INFO  @ Thu, 13 Apr 2017 18:41:50:  72000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  73000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  74000000 
INFO  @ Thu, 13 Apr 2017 18:41:56:  75000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  76000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  77000000 
INFO  @ Thu, 13 Apr 2017 18:42:02:  78000000 
INFO  @ Thu, 13 Apr 2017 18:42:04:  79000000 
INFO  @ Thu, 13 Apr 2017 18:42:05:  80000000 
INFO  @ Thu, 13 Apr 2017 18:42:07:  81000000 
INFO  @ Thu, 13 Apr 2017 18:42:09:  82000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  83000000 
INFO  @ Thu, 13 Apr 2017 18:42:13:  84000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  85000000 
INFO  @ Thu, 13 Apr 2017 18:42:17:  86000000 
INFO  @ Thu, 13 Apr 2017 18:42:18:  87000000 
INFO  @ Thu, 13 Apr 2017 18:42:20:  88000000 
INFO  @ Thu, 13 Apr 2017 18:42:22:  89000000 
INFO  @ Thu, 13 Apr 2017 18:42:24:  90000000 
INFO  @ Thu, 13 Apr 2017 18:42:26:  91000000 
INFO  @ Thu, 13 Apr 2017 18:42:28:  92000000 
INFO  @ Thu, 13 Apr 2017 18:42:30:  93000000 
INFO  @ Thu, 13 Apr 2017 18:42:32:  94000000 
INFO  @ Thu, 13 Apr 2017 18:42:34:  95000000 
INFO  @ Thu, 13 Apr 2017 18:42:35:  96000000 
INFO  @ Thu, 13 Apr 2017 18:42:37:  97000000 
INFO  @ Thu, 13 Apr 2017 18:42:39:  98000000 
INFO  @ Thu, 13 Apr 2017 18:42:41:  99000000 
INFO  @ Thu, 13 Apr 2017 18:42:43: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:42:43: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:42:43: #1  total tags in treatment: 45202518 
INFO  @ Thu, 13 Apr 2017 18:42:43: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:42:43: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:42:43: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:42:43: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:42:43: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:42:43: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:42:43: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:42:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:52:02: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:59:34: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:59:37: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:59:39: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:59:40: Done!

Num	2
ID	task.callpeak_macs2.macs2_g_b_ppr1.line_155.id_11
Name	macs2 g/b ppr1
Thread	thread_Root
PID	46964

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

Start	2017-04-13 18:37:47
End	2017-04-13 18:50:09
Elapsed	00:12:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 210 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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--------------------
47348 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 210 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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 18:38:01: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:01: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:03:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:05:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:06:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:08:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:09:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:11:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:12:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:14:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:15:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:17:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:19:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:24:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:30:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:38: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:40:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:58:  56000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  57000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  58000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  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 18:40:26:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:28:  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 18:40:34:  82000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  83000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  84000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  85000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  86000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  87000000 
INFO  @ Thu, 13 Apr 2017 18:40:43:  88000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  89000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  90000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  91000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  92000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  93000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  94000000 
INFO  @ Thu, 13 Apr 2017 18:40:53:  95000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  96000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  97000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  98000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:00: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:41:00: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:41:00: #1  total tags in treatment: 22601260 
INFO  @ Thu, 13 Apr 2017 18:41:00: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:41:00: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:41:00: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:41:00: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:41:00: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:41:00: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:41:00: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:41:00: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:46:01: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:49:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:49:58: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:50:00: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:50:02: Done!

Num	3
ID	task.callpeak_macs2.macs2_g_b_ppr2.line_155.id_12
Name	macs2 g/b ppr2
Thread	thread_Root
PID	46966

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

Start	2017-04-13 18:37:48
End	2017-04-13 18:50:13
Elapsed	00:12:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 210 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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--------------------
47350 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:01: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 210 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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 18:38:01: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:01: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:03:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:04:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:06:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:07:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:09:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:10:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:12:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:13:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:15:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:17:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:19:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:38: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:40:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:58:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  56000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  57000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  58000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  72000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  73000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  74000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  75000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  77000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  78000000 
INFO  @ Thu, 13 Apr 2017 18:40:34:  79000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  80000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  81000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  82000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  83000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  84000000 
INFO  @ Thu, 13 Apr 2017 18:40:43:  85000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  86000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  87000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  88000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  89000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  90000000 
INFO  @ Thu, 13 Apr 2017 18:40:53:  91000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  92000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  93000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  94000000 
INFO  @ Thu, 13 Apr 2017 18:40:59:  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 18:41:04:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:06: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:41:06: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:41:06: #1  total tags in treatment: 22601258 
INFO  @ Thu, 13 Apr 2017 18:41:06: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:41:06: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:41:06: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:41:06: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:41:06: #2 Use 210 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:41:06: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:41:06: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:41:06: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:46:06: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:50:01: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:50:03: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:50:05: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:50:06: Done!

Num	4
ID	task.callpeak_macs2.macs2_g_b_rep1.line_155.id_13
Name	macs2 g/b rep1
Thread	thread_Root
PID	46967

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

Start	2017-04-13 18:37:50
End	2017-04-13 18:57:47
Elapsed	00:19:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 195 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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--------------------
13996 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 195 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.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 18:38:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:04:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:06:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:08:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:11:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:13:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:15:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:17:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:19:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:38:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:55: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:57:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:59:  2000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  3000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  4000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  5000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  6000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  7000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:18:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  34000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  35000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  36000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  37000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  38000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  39000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  40000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  41000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  42000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  45000000 
INFO  @ Thu, 13 Apr 2017 18:40:22:  46000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  47000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  48000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  51000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  52000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  53000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  54000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  55000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  56000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  57000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  58000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:59:  66000000 
INFO  @ Thu, 13 Apr 2017 18:41:01:  67000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  68000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  69000000 
INFO  @ Thu, 13 Apr 2017 18:41:07:  70000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  71000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  72000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  73000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  74000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  75000000 
INFO  @ Thu, 13 Apr 2017 18:41:18:  76000000 
INFO  @ Thu, 13 Apr 2017 18:41:20:  77000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  78000000 
INFO  @ Thu, 13 Apr 2017 18:41:24:  79000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  80000000 
INFO  @ Thu, 13 Apr 2017 18:41:28:  81000000 
INFO  @ Thu, 13 Apr 2017 18:41:30:  82000000 
INFO  @ Thu, 13 Apr 2017 18:41:32:  83000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  84000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  85000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  86000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  87000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  88000000 
INFO  @ Thu, 13 Apr 2017 18:41:43:  89000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  90000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  91000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  92000000 
INFO  @ Thu, 13 Apr 2017 18:41:50:  93000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  94000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  95000000 
INFO  @ Thu, 13 Apr 2017 18:41:56:  96000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  97000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  98000000 
INFO  @ Thu, 13 Apr 2017 18:42:02:  99000000 
INFO  @ Thu, 13 Apr 2017 18:42:04: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:42:04: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:42:04: #1  total tags in treatment: 24587032 
INFO  @ Thu, 13 Apr 2017 18:42:04: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:42:04: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:42:04: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:42:04: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:42:04: #2 Use 195 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:42:04: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:42:04: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:42:04: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:50:16: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:57:27: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:57:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:57:35: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:57:37: 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	46972

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

Start	2017-04-13 18:37:52
End	2017-04-13 18:57:45
Elapsed	00:19:52
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 195 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.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--------------------
14426 (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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 195 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF888DOH.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 18:38:21:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:43: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:38:45:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:52:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:58:  39000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  40000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  41000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  42000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  45000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  46000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  47000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  48000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  51000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  52000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  53000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  54000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  55000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  56000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  57000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  58000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  70000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  71000000 
INFO  @ Thu, 13 Apr 2017 18:41:02:  72000000 
INFO  @ Thu, 13 Apr 2017 18:41:04:  73000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  74000000 
INFO  @ Thu, 13 Apr 2017 18:41:07:  75000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  76000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  77000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  78000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  79000000 
INFO  @ Thu, 13 Apr 2017 18:41:17:  80000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  81000000 
INFO  @ Thu, 13 Apr 2017 18:41:21:  82000000 
INFO  @ Thu, 13 Apr 2017 18:41:23:  83000000 
INFO  @ Thu, 13 Apr 2017 18:41:25:  84000000 
INFO  @ Thu, 13 Apr 2017 18:41:27:  85000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  86000000 
INFO  @ Thu, 13 Apr 2017 18:41:31:  87000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  88000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  89000000 
INFO  @ Thu, 13 Apr 2017 18:41:36:  90000000 
INFO  @ Thu, 13 Apr 2017 18:41:38:  91000000 
INFO  @ Thu, 13 Apr 2017 18:41:40:  92000000 
INFO  @ Thu, 13 Apr 2017 18:41:42:  93000000 
INFO  @ Thu, 13 Apr 2017 18:41:44:  94000000 
INFO  @ Thu, 13 Apr 2017 18:41:46:  95000000 
INFO  @ Thu, 13 Apr 2017 18:41:48:  96000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  97000000 
INFO  @ Thu, 13 Apr 2017 18:41:51:  98000000 
INFO  @ Thu, 13 Apr 2017 18:41:53:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:55: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:41:55: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:41:55: #1  total tags in treatment: 12293516 
INFO  @ Thu, 13 Apr 2017 18:41:55: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:41:55: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:41:55: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:41:55: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:41:55: #2 Use 195 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:41:55: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:41:55: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:41:55: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:49:37: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:57:15: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:57:21: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:57:26: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF888DOH.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:57:31: 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	47013

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

Start	2017-04-13 18:50:12
End	2017-04-13 19:02:14
Elapsed	00:12:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 195 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.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--------------------
21279 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:50:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 195 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF888DOH.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 18:50:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:50:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:50:33:  1000000 
INFO  @ Thu, 13 Apr 2017 18:50:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:50:36:  3000000 
INFO  @ Thu, 13 Apr 2017 18:50:38:  4000000 
INFO  @ Thu, 13 Apr 2017 18:50:40:  5000000 
INFO  @ Thu, 13 Apr 2017 18:50:41:  6000000 
INFO  @ Thu, 13 Apr 2017 18:50:43:  7000000 
INFO  @ Thu, 13 Apr 2017 18:50:44:  8000000 
INFO  @ Thu, 13 Apr 2017 18:50:46:  9000000 
INFO  @ Thu, 13 Apr 2017 18:50:48:  10000000 
INFO  @ Thu, 13 Apr 2017 18:50:49:  11000000 
INFO  @ Thu, 13 Apr 2017 18:50:51:  12000000 
INFO  @ Thu, 13 Apr 2017 18:50:52: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:50:53:  1000000 
INFO  @ Thu, 13 Apr 2017 18:50:55:  2000000 
INFO  @ Thu, 13 Apr 2017 18:50:57:  3000000 
INFO  @ Thu, 13 Apr 2017 18:50:58:  4000000 
INFO  @ Thu, 13 Apr 2017 18:50:59:  5000000 
INFO  @ Thu, 13 Apr 2017 18:51:01:  6000000 
INFO  @ Thu, 13 Apr 2017 18:51:02:  7000000 
INFO  @ Thu, 13 Apr 2017 18:51:04:  8000000 
INFO  @ Thu, 13 Apr 2017 18:51:05:  9000000 
INFO  @ Thu, 13 Apr 2017 18:51:07:  10000000 
INFO  @ Thu, 13 Apr 2017 18:51:08:  11000000 
INFO  @ Thu, 13 Apr 2017 18:51:09:  12000000 
INFO  @ Thu, 13 Apr 2017 18:51:11:  13000000 
INFO  @ Thu, 13 Apr 2017 18:51:12:  14000000 
INFO  @ Thu, 13 Apr 2017 18:51:14:  15000000 
INFO  @ Thu, 13 Apr 2017 18:51:15:  16000000 
INFO  @ Thu, 13 Apr 2017 18:51:17:  17000000 
INFO  @ Thu, 13 Apr 2017 18:51:18:  18000000 
INFO  @ Thu, 13 Apr 2017 18:51:20:  19000000 
INFO  @ Thu, 13 Apr 2017 18:51:21:  20000000 
INFO  @ Thu, 13 Apr 2017 18:51:23:  21000000 
INFO  @ Thu, 13 Apr 2017 18:51:24:  22000000 
INFO  @ Thu, 13 Apr 2017 18:51:26:  23000000 
INFO  @ Thu, 13 Apr 2017 18:51:27:  24000000 
INFO  @ Thu, 13 Apr 2017 18:51:29:  25000000 
INFO  @ Thu, 13 Apr 2017 18:51:30:  26000000 
INFO  @ Thu, 13 Apr 2017 18:51:32:  27000000 
INFO  @ Thu, 13 Apr 2017 18:51:33:  28000000 
INFO  @ Thu, 13 Apr 2017 18:51:35:  29000000 
INFO  @ Thu, 13 Apr 2017 18:51:36:  30000000 
INFO  @ Thu, 13 Apr 2017 18:51:37:  31000000 
INFO  @ Thu, 13 Apr 2017 18:51:39:  32000000 
INFO  @ Thu, 13 Apr 2017 18:51:40:  33000000 
INFO  @ Thu, 13 Apr 2017 18:51:42:  34000000 
INFO  @ Thu, 13 Apr 2017 18:51:43:  35000000 
INFO  @ Thu, 13 Apr 2017 18:51:45:  36000000 
INFO  @ Thu, 13 Apr 2017 18:51:46:  37000000 
INFO  @ Thu, 13 Apr 2017 18:51:48:  38000000 
INFO  @ Thu, 13 Apr 2017 18:51:49:  39000000 
INFO  @ Thu, 13 Apr 2017 18:51:51:  40000000 
INFO  @ Thu, 13 Apr 2017 18:51:52:  41000000 
INFO  @ Thu, 13 Apr 2017 18:51:54:  42000000 
INFO  @ Thu, 13 Apr 2017 18:51:55:  43000000 
INFO  @ Thu, 13 Apr 2017 18:51:56:  44000000 
INFO  @ Thu, 13 Apr 2017 18:51:58:  45000000 
INFO  @ Thu, 13 Apr 2017 18:51:59:  46000000 
INFO  @ Thu, 13 Apr 2017 18:52:01:  47000000 
INFO  @ Thu, 13 Apr 2017 18:52:02:  48000000 
INFO  @ Thu, 13 Apr 2017 18:52:03:  49000000 
INFO  @ Thu, 13 Apr 2017 18:52:05:  50000000 
INFO  @ Thu, 13 Apr 2017 18:52:06:  51000000 
INFO  @ Thu, 13 Apr 2017 18:52:08:  52000000 
INFO  @ Thu, 13 Apr 2017 18:52:09:  53000000 
INFO  @ Thu, 13 Apr 2017 18:52:11:  54000000 
INFO  @ Thu, 13 Apr 2017 18:52:12:  55000000 
INFO  @ Thu, 13 Apr 2017 18:52:13:  56000000 
INFO  @ Thu, 13 Apr 2017 18:52:15:  57000000 
INFO  @ Thu, 13 Apr 2017 18:52:16:  58000000 
INFO  @ Thu, 13 Apr 2017 18:52:18:  59000000 
INFO  @ Thu, 13 Apr 2017 18:52:19:  60000000 
INFO  @ Thu, 13 Apr 2017 18:52:21:  61000000 
INFO  @ Thu, 13 Apr 2017 18:52:22:  62000000 
INFO  @ Thu, 13 Apr 2017 18:52:23:  63000000 
INFO  @ Thu, 13 Apr 2017 18:52:25:  64000000 
INFO  @ Thu, 13 Apr 2017 18:52:26:  65000000 
INFO  @ Thu, 13 Apr 2017 18:52:28:  66000000 
INFO  @ Thu, 13 Apr 2017 18:52:29:  67000000 
INFO  @ Thu, 13 Apr 2017 18:52:31:  68000000 
INFO  @ Thu, 13 Apr 2017 18:52:32:  69000000 
INFO  @ Thu, 13 Apr 2017 18:52:33:  70000000 
INFO  @ Thu, 13 Apr 2017 18:52:35:  71000000 
INFO  @ Thu, 13 Apr 2017 18:52:36:  72000000 
INFO  @ Thu, 13 Apr 2017 18:52:38:  73000000 
INFO  @ Thu, 13 Apr 2017 18:52:39:  74000000 
INFO  @ Thu, 13 Apr 2017 18:52:41:  75000000 
INFO  @ Thu, 13 Apr 2017 18:52:42:  76000000 
INFO  @ Thu, 13 Apr 2017 18:52:43:  77000000 
INFO  @ Thu, 13 Apr 2017 18:52:45:  78000000 
INFO  @ Thu, 13 Apr 2017 18:52:46:  79000000 
INFO  @ Thu, 13 Apr 2017 18:52:48:  80000000 
INFO  @ Thu, 13 Apr 2017 18:52:49:  81000000 
INFO  @ Thu, 13 Apr 2017 18:52:50:  82000000 
INFO  @ Thu, 13 Apr 2017 18:52:52:  83000000 
INFO  @ Thu, 13 Apr 2017 18:52:53:  84000000 
INFO  @ Thu, 13 Apr 2017 18:52:55:  85000000 
INFO  @ Thu, 13 Apr 2017 18:52:56:  86000000 
INFO  @ Thu, 13 Apr 2017 18:52:58:  87000000 
INFO  @ Thu, 13 Apr 2017 18:52:59:  88000000 
INFO  @ Thu, 13 Apr 2017 18:53:00:  89000000 
INFO  @ Thu, 13 Apr 2017 18:53:02:  90000000 
INFO  @ Thu, 13 Apr 2017 18:53:03:  91000000 
INFO  @ Thu, 13 Apr 2017 18:53:05:  92000000 
INFO  @ Thu, 13 Apr 2017 18:53:06:  93000000 
INFO  @ Thu, 13 Apr 2017 18:53:07:  94000000 
INFO  @ Thu, 13 Apr 2017 18:53:09:  95000000 
INFO  @ Thu, 13 Apr 2017 18:53:10:  96000000 
INFO  @ Thu, 13 Apr 2017 18:53:12:  97000000 
INFO  @ Thu, 13 Apr 2017 18:53:13:  98000000 
INFO  @ Thu, 13 Apr 2017 18:53:14:  99000000 
INFO  @ Thu, 13 Apr 2017 18:53:16: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:53:16: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:53:16: #1  total tags in treatment: 12293516 
INFO  @ Thu, 13 Apr 2017 18:53:16: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:53:16: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:53:16: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:53:16: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:53:16: #2 Use 195 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:53:16: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:53:16: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:53:16: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:57:51: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:01:55: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:01:59: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:02:02: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF888DOH.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:02:04: Done!

Num	7
ID	task.callpeak_macs2.macs2_g_b_rep2.line_155.id_16
Name	macs2 g/b rep2
Thread	thread_Root
PID	47014

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

Start	2017-04-13 18:50:15
End	2017-04-13 19:02:21
Elapsed	00:12:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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/EGR2_MACS2/out/align/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 225 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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--------------------
21280 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:50:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 225 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.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 18:50:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:50:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:50:33:  1000000 
INFO  @ Thu, 13 Apr 2017 18:50:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:50:36:  3000000 
INFO  @ Thu, 13 Apr 2017 18:50:38:  4000000 
INFO  @ Thu, 13 Apr 2017 18:50:40:  5000000 
INFO  @ Thu, 13 Apr 2017 18:50:41:  6000000 
INFO  @ Thu, 13 Apr 2017 18:50:43:  7000000 
INFO  @ Thu, 13 Apr 2017 18:50:44:  8000000 
INFO  @ Thu, 13 Apr 2017 18:50:46:  9000000 
INFO  @ Thu, 13 Apr 2017 18:50:47:  10000000 
INFO  @ Thu, 13 Apr 2017 18:50:49:  11000000 
INFO  @ Thu, 13 Apr 2017 18:50:50:  12000000 
INFO  @ Thu, 13 Apr 2017 18:50:52:  13000000 
INFO  @ Thu, 13 Apr 2017 18:50:53:  14000000 
INFO  @ Thu, 13 Apr 2017 18:50:55:  15000000 
INFO  @ Thu, 13 Apr 2017 18:50:56:  16000000 
INFO  @ Thu, 13 Apr 2017 18:50:58:  17000000 
INFO  @ Thu, 13 Apr 2017 18:50:59:  18000000 
INFO  @ Thu, 13 Apr 2017 18:51:01:  19000000 
INFO  @ Thu, 13 Apr 2017 18:51:02:  20000000 
INFO  @ Thu, 13 Apr 2017 18:51:04: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:51:06:  1000000 
INFO  @ Thu, 13 Apr 2017 18:51:07:  2000000 
INFO  @ Thu, 13 Apr 2017 18:51:08:  3000000 
INFO  @ Thu, 13 Apr 2017 18:51:10:  4000000 
INFO  @ Thu, 13 Apr 2017 18:51:11:  5000000 
INFO  @ Thu, 13 Apr 2017 18:51:13:  6000000 
INFO  @ Thu, 13 Apr 2017 18:51:14:  7000000 
INFO  @ Thu, 13 Apr 2017 18:51:16:  8000000 
INFO  @ Thu, 13 Apr 2017 18:51:17:  9000000 
INFO  @ Thu, 13 Apr 2017 18:51:18:  10000000 
INFO  @ Thu, 13 Apr 2017 18:51:20:  11000000 
INFO  @ Thu, 13 Apr 2017 18:51:21:  12000000 
INFO  @ Thu, 13 Apr 2017 18:51:23:  13000000 
INFO  @ Thu, 13 Apr 2017 18:51:24:  14000000 
INFO  @ Thu, 13 Apr 2017 18:51:25:  15000000 
INFO  @ Thu, 13 Apr 2017 18:51:27:  16000000 
INFO  @ Thu, 13 Apr 2017 18:51:28:  17000000 
INFO  @ Thu, 13 Apr 2017 18:51:29:  18000000 
INFO  @ Thu, 13 Apr 2017 18:51:31:  19000000 
INFO  @ Thu, 13 Apr 2017 18:51:32:  20000000 
INFO  @ Thu, 13 Apr 2017 18:51:34:  21000000 
INFO  @ Thu, 13 Apr 2017 18:51:35:  22000000 
INFO  @ Thu, 13 Apr 2017 18:51:36:  23000000 
INFO  @ Thu, 13 Apr 2017 18:51:38:  24000000 
INFO  @ Thu, 13 Apr 2017 18:51:39:  25000000 
INFO  @ Thu, 13 Apr 2017 18:51:41:  26000000 
INFO  @ Thu, 13 Apr 2017 18:51:42:  27000000 
INFO  @ Thu, 13 Apr 2017 18:51:43:  28000000 
INFO  @ Thu, 13 Apr 2017 18:51:45:  29000000 
INFO  @ Thu, 13 Apr 2017 18:51:46:  30000000 
INFO  @ Thu, 13 Apr 2017 18:51:47:  31000000 
INFO  @ Thu, 13 Apr 2017 18:51:49:  32000000 
INFO  @ Thu, 13 Apr 2017 18:51:50:  33000000 
INFO  @ Thu, 13 Apr 2017 18:51:52:  34000000 
INFO  @ Thu, 13 Apr 2017 18:51:53:  35000000 
INFO  @ Thu, 13 Apr 2017 18:51:54:  36000000 
INFO  @ Thu, 13 Apr 2017 18:51:56:  37000000 
INFO  @ Thu, 13 Apr 2017 18:51:57:  38000000 
INFO  @ Thu, 13 Apr 2017 18:51:59:  39000000 
INFO  @ Thu, 13 Apr 2017 18:52:00:  40000000 
INFO  @ Thu, 13 Apr 2017 18:52:01:  41000000 
INFO  @ Thu, 13 Apr 2017 18:52:03:  42000000 
INFO  @ Thu, 13 Apr 2017 18:52:04:  43000000 
INFO  @ Thu, 13 Apr 2017 18:52:05:  44000000 
INFO  @ Thu, 13 Apr 2017 18:52:07:  45000000 
INFO  @ Thu, 13 Apr 2017 18:52:08:  46000000 
INFO  @ Thu, 13 Apr 2017 18:52:10:  47000000 
INFO  @ Thu, 13 Apr 2017 18:52:11:  48000000 
INFO  @ Thu, 13 Apr 2017 18:52:12:  49000000 
INFO  @ Thu, 13 Apr 2017 18:52:14:  50000000 
INFO  @ Thu, 13 Apr 2017 18:52:15:  51000000 
INFO  @ Thu, 13 Apr 2017 18:52:17:  52000000 
INFO  @ Thu, 13 Apr 2017 18:52:18:  53000000 
INFO  @ Thu, 13 Apr 2017 18:52:20:  54000000 
INFO  @ Thu, 13 Apr 2017 18:52:21:  55000000 
INFO  @ Thu, 13 Apr 2017 18:52:23:  56000000 
INFO  @ Thu, 13 Apr 2017 18:52:24:  57000000 
INFO  @ Thu, 13 Apr 2017 18:52:25:  58000000 
INFO  @ Thu, 13 Apr 2017 18:52:27:  59000000 
INFO  @ Thu, 13 Apr 2017 18:52:29:  60000000 
INFO  @ Thu, 13 Apr 2017 18:52:30:  61000000 
INFO  @ Thu, 13 Apr 2017 18:52:32:  62000000 
INFO  @ Thu, 13 Apr 2017 18:52:33:  63000000 
INFO  @ Thu, 13 Apr 2017 18:52:34:  64000000 
INFO  @ Thu, 13 Apr 2017 18:52:36:  65000000 
INFO  @ Thu, 13 Apr 2017 18:52:37:  66000000 
INFO  @ Thu, 13 Apr 2017 18:52:39:  67000000 
INFO  @ Thu, 13 Apr 2017 18:52:40:  68000000 
INFO  @ Thu, 13 Apr 2017 18:52:41:  69000000 
INFO  @ Thu, 13 Apr 2017 18:52:43:  70000000 
INFO  @ Thu, 13 Apr 2017 18:52:44:  71000000 
INFO  @ Thu, 13 Apr 2017 18:52:46:  72000000 
INFO  @ Thu, 13 Apr 2017 18:52:47:  73000000 
INFO  @ Thu, 13 Apr 2017 18:52:48:  74000000 
INFO  @ Thu, 13 Apr 2017 18:52:50:  75000000 
INFO  @ Thu, 13 Apr 2017 18:52:51:  76000000 
INFO  @ Thu, 13 Apr 2017 18:52:53:  77000000 
INFO  @ Thu, 13 Apr 2017 18:52:54:  78000000 
INFO  @ Thu, 13 Apr 2017 18:52:55:  79000000 
INFO  @ Thu, 13 Apr 2017 18:52:57:  80000000 
INFO  @ Thu, 13 Apr 2017 18:52:58:  81000000 
INFO  @ Thu, 13 Apr 2017 18:52:59:  82000000 
INFO  @ Thu, 13 Apr 2017 18:53:01:  83000000 
INFO  @ Thu, 13 Apr 2017 18:53:02:  84000000 
INFO  @ Thu, 13 Apr 2017 18:53:04:  85000000 
INFO  @ Thu, 13 Apr 2017 18:53:05:  86000000 
INFO  @ Thu, 13 Apr 2017 18:53:06:  87000000 
INFO  @ Thu, 13 Apr 2017 18:53:08:  88000000 
INFO  @ Thu, 13 Apr 2017 18:53:09:  89000000 
INFO  @ Thu, 13 Apr 2017 18:53:11:  90000000 
INFO  @ Thu, 13 Apr 2017 18:53:12:  91000000 
INFO  @ Thu, 13 Apr 2017 18:53:13:  92000000 
INFO  @ Thu, 13 Apr 2017 18:53:15:  93000000 
INFO  @ Thu, 13 Apr 2017 18:53:16:  94000000 
INFO  @ Thu, 13 Apr 2017 18:53:18:  95000000 
INFO  @ Thu, 13 Apr 2017 18:53:19:  96000000 
INFO  @ Thu, 13 Apr 2017 18:53:21:  97000000 
INFO  @ Thu, 13 Apr 2017 18:53:22:  98000000 
INFO  @ Thu, 13 Apr 2017 18:53:23:  99000000 
INFO  @ Thu, 13 Apr 2017 18:53:25: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:53:25: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:53:25: #1  total tags in treatment: 20615486 
INFO  @ Thu, 13 Apr 2017 18:53:25: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:53:25: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:53:25: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:53:25: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:53:25: #2 Use 225 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:53:25: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:53:25: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:53:25: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:58:12: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:02:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:02:11: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:02:13: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:02:14: 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	47026

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

Start	2017-04-13 18:57:50
End	2017-04-13 19:09:45
Elapsed	00:11:55
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 225 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.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--------------------
39806 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:58:00: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 225 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF234ALA.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 18:58:00: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:58:00: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:58:02:  1000000 
INFO  @ Thu, 13 Apr 2017 18:58:03:  2000000 
INFO  @ Thu, 13 Apr 2017 18:58:05:  3000000 
INFO  @ Thu, 13 Apr 2017 18:58:06:  4000000 
INFO  @ Thu, 13 Apr 2017 18:58:08:  5000000 
INFO  @ Thu, 13 Apr 2017 18:58:09:  6000000 
INFO  @ Thu, 13 Apr 2017 18:58:11:  7000000 
INFO  @ Thu, 13 Apr 2017 18:58:12:  8000000 
INFO  @ Thu, 13 Apr 2017 18:58:14:  9000000 
INFO  @ Thu, 13 Apr 2017 18:58:15:  10000000 
INFO  @ Thu, 13 Apr 2017 18:58:16: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:58:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:58:19:  2000000 
INFO  @ Thu, 13 Apr 2017 18:58:21:  3000000 
INFO  @ Thu, 13 Apr 2017 18:58:22:  4000000 
INFO  @ Thu, 13 Apr 2017 18:58:23:  5000000 
INFO  @ Thu, 13 Apr 2017 18:58:25:  6000000 
INFO  @ Thu, 13 Apr 2017 18:58:26:  7000000 
INFO  @ Thu, 13 Apr 2017 18:58:28:  8000000 
INFO  @ Thu, 13 Apr 2017 18:58:29:  9000000 
INFO  @ Thu, 13 Apr 2017 18:58:30:  10000000 
INFO  @ Thu, 13 Apr 2017 18:58:32:  11000000 
INFO  @ Thu, 13 Apr 2017 18:58:33:  12000000 
INFO  @ Thu, 13 Apr 2017 18:58:35:  13000000 
INFO  @ Thu, 13 Apr 2017 18:58:36:  14000000 
INFO  @ Thu, 13 Apr 2017 18:58:37:  15000000 
INFO  @ Thu, 13 Apr 2017 18:58:39:  16000000 
INFO  @ Thu, 13 Apr 2017 18:58:40:  17000000 
INFO  @ Thu, 13 Apr 2017 18:58:41:  18000000 
INFO  @ Thu, 13 Apr 2017 18:58:43:  19000000 
INFO  @ Thu, 13 Apr 2017 18:58:44:  20000000 
INFO  @ Thu, 13 Apr 2017 18:58:46:  21000000 
INFO  @ Thu, 13 Apr 2017 18:58:47:  22000000 
INFO  @ Thu, 13 Apr 2017 18:58:48:  23000000 
INFO  @ Thu, 13 Apr 2017 18:58:50:  24000000 
INFO  @ Thu, 13 Apr 2017 18:58:51:  25000000 
INFO  @ Thu, 13 Apr 2017 18:58:53:  26000000 
INFO  @ Thu, 13 Apr 2017 18:58:54:  27000000 
INFO  @ Thu, 13 Apr 2017 18:58:55:  28000000 
INFO  @ Thu, 13 Apr 2017 18:58:57:  29000000 
INFO  @ Thu, 13 Apr 2017 18:58:58:  30000000 
INFO  @ Thu, 13 Apr 2017 18:58:59:  31000000 
INFO  @ Thu, 13 Apr 2017 18:59:01:  32000000 
INFO  @ Thu, 13 Apr 2017 18:59:02:  33000000 
INFO  @ Thu, 13 Apr 2017 18:59:04:  34000000 
INFO  @ Thu, 13 Apr 2017 18:59:05:  35000000 
INFO  @ Thu, 13 Apr 2017 18:59:06:  36000000 
INFO  @ Thu, 13 Apr 2017 18:59:08:  37000000 
INFO  @ Thu, 13 Apr 2017 18:59:09:  38000000 
INFO  @ Thu, 13 Apr 2017 18:59:11:  39000000 
INFO  @ Thu, 13 Apr 2017 18:59:12:  40000000 
INFO  @ Thu, 13 Apr 2017 18:59:13:  41000000 
INFO  @ Thu, 13 Apr 2017 18:59:15:  42000000 
INFO  @ Thu, 13 Apr 2017 18:59:16:  43000000 
INFO  @ Thu, 13 Apr 2017 18:59:18:  44000000 
INFO  @ Thu, 13 Apr 2017 18:59:19:  45000000 
INFO  @ Thu, 13 Apr 2017 18:59:20:  46000000 
INFO  @ Thu, 13 Apr 2017 18:59:22:  47000000 
INFO  @ Thu, 13 Apr 2017 18:59:23:  48000000 
INFO  @ Thu, 13 Apr 2017 18:59:25:  49000000 
INFO  @ Thu, 13 Apr 2017 18:59:26:  50000000 
INFO  @ Thu, 13 Apr 2017 18:59:27:  51000000 
INFO  @ Thu, 13 Apr 2017 18:59:29:  52000000 
INFO  @ Thu, 13 Apr 2017 18:59:30:  53000000 
INFO  @ Thu, 13 Apr 2017 18:59:32:  54000000 
INFO  @ Thu, 13 Apr 2017 18:59:33:  55000000 
INFO  @ Thu, 13 Apr 2017 18:59:34:  56000000 
INFO  @ Thu, 13 Apr 2017 18:59:36:  57000000 
INFO  @ Thu, 13 Apr 2017 18:59:37:  58000000 
INFO  @ Thu, 13 Apr 2017 18:59:39:  59000000 
INFO  @ Thu, 13 Apr 2017 18:59:40:  60000000 
INFO  @ Thu, 13 Apr 2017 18:59:41:  61000000 
INFO  @ Thu, 13 Apr 2017 18:59:43:  62000000 
INFO  @ Thu, 13 Apr 2017 18:59:44:  63000000 
INFO  @ Thu, 13 Apr 2017 18:59:46:  64000000 
INFO  @ Thu, 13 Apr 2017 18:59:47:  65000000 
INFO  @ Thu, 13 Apr 2017 18:59:48:  66000000 
INFO  @ Thu, 13 Apr 2017 18:59:50:  67000000 
INFO  @ Thu, 13 Apr 2017 18:59:51:  68000000 
INFO  @ Thu, 13 Apr 2017 18:59:53:  69000000 
INFO  @ Thu, 13 Apr 2017 18:59:54:  70000000 
INFO  @ Thu, 13 Apr 2017 18:59:55:  71000000 
INFO  @ Thu, 13 Apr 2017 18:59:57:  72000000 
INFO  @ Thu, 13 Apr 2017 18:59:58:  73000000 
INFO  @ Thu, 13 Apr 2017 18:59:59:  74000000 
INFO  @ Thu, 13 Apr 2017 19:00:01:  75000000 
INFO  @ Thu, 13 Apr 2017 19:00:02:  76000000 
INFO  @ Thu, 13 Apr 2017 19:00:04:  77000000 
INFO  @ Thu, 13 Apr 2017 19:00:05:  78000000 
INFO  @ Thu, 13 Apr 2017 19:00:06:  79000000 
INFO  @ Thu, 13 Apr 2017 19:00:08:  80000000 
INFO  @ Thu, 13 Apr 2017 19:00:09:  81000000 
INFO  @ Thu, 13 Apr 2017 19:00:11:  82000000 
INFO  @ Thu, 13 Apr 2017 19:00:12:  83000000 
INFO  @ Thu, 13 Apr 2017 19:00:13:  84000000 
INFO  @ Thu, 13 Apr 2017 19:00:15:  85000000 
INFO  @ Thu, 13 Apr 2017 19:00:16:  86000000 
INFO  @ Thu, 13 Apr 2017 19:00:18:  87000000 
INFO  @ Thu, 13 Apr 2017 19:00:19:  88000000 
INFO  @ Thu, 13 Apr 2017 19:00:20:  89000000 
INFO  @ Thu, 13 Apr 2017 19:00:22:  90000000 
INFO  @ Thu, 13 Apr 2017 19:00:23:  91000000 
INFO  @ Thu, 13 Apr 2017 19:00:25:  92000000 
INFO  @ Thu, 13 Apr 2017 19:00:26:  93000000 
INFO  @ Thu, 13 Apr 2017 19:00:27:  94000000 
INFO  @ Thu, 13 Apr 2017 19:00:29:  95000000 
INFO  @ Thu, 13 Apr 2017 19:00:30:  96000000 
INFO  @ Thu, 13 Apr 2017 19:00:32:  97000000 
INFO  @ Thu, 13 Apr 2017 19:00:33:  98000000 
INFO  @ Thu, 13 Apr 2017 19:00:34:  99000000 
INFO  @ Thu, 13 Apr 2017 19:00:36: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 19:00:36: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 19:00:36: #1  total tags in treatment: 10307744 
INFO  @ Thu, 13 Apr 2017 19:00:36: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 19:00:36: #1 finished! 
INFO  @ Thu, 13 Apr 2017 19:00:36: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 19:00:36: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 19:00:36: #2 Use 225 as fragment length 
INFO  @ Thu, 13 Apr 2017 19:00:36: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 19:00:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 19:00:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:05:09: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:09:28: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:09:31: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:09:34: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:09:37: 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	47027

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

Start	2017-04-13 18:57:52
End	2017-04-13 19:13:29
Elapsed	00:15:37
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 225 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.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--------------------
15423 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:58:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 225 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF234ALA.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 18:58:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:58:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:58:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:58:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:58:22:  3000000 
INFO  @ Thu, 13 Apr 2017 18:58:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:58:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:58:27:  6000000 
INFO  @ Thu, 13 Apr 2017 18:58:28:  7000000 
INFO  @ Thu, 13 Apr 2017 18:58:30:  8000000 
INFO  @ Thu, 13 Apr 2017 18:58:31:  9000000 
INFO  @ Thu, 13 Apr 2017 18:58:33:  10000000 
INFO  @ Thu, 13 Apr 2017 18:58:34: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:58:35:  1000000 
INFO  @ Thu, 13 Apr 2017 18:58:37:  2000000 
INFO  @ Thu, 13 Apr 2017 18:58:38:  3000000 
INFO  @ Thu, 13 Apr 2017 18:58:40:  4000000 
INFO  @ Thu, 13 Apr 2017 18:58:41:  5000000 
INFO  @ Thu, 13 Apr 2017 18:58:43:  6000000 
INFO  @ Thu, 13 Apr 2017 18:58:44:  7000000 
INFO  @ Thu, 13 Apr 2017 18:58:46:  8000000 
INFO  @ Thu, 13 Apr 2017 18:58:47:  9000000 
INFO  @ Thu, 13 Apr 2017 18:58:48:  10000000 
INFO  @ Thu, 13 Apr 2017 18:58:50:  11000000 
INFO  @ Thu, 13 Apr 2017 18:58:51:  12000000 
INFO  @ Thu, 13 Apr 2017 18:58:53:  13000000 
INFO  @ Thu, 13 Apr 2017 18:58:54:  14000000 
INFO  @ Thu, 13 Apr 2017 18:58:56:  15000000 
INFO  @ Thu, 13 Apr 2017 18:58:57:  16000000 
INFO  @ Thu, 13 Apr 2017 18:58:59:  17000000 
INFO  @ Thu, 13 Apr 2017 18:59:00:  18000000 
INFO  @ Thu, 13 Apr 2017 18:59:01:  19000000 
INFO  @ Thu, 13 Apr 2017 18:59:03:  20000000 
INFO  @ Thu, 13 Apr 2017 18:59:04:  21000000 
INFO  @ Thu, 13 Apr 2017 18:59:06:  22000000 
INFO  @ Thu, 13 Apr 2017 18:59:07:  23000000 
INFO  @ Thu, 13 Apr 2017 18:59:09:  24000000 
INFO  @ Thu, 13 Apr 2017 18:59:10:  25000000 
INFO  @ Thu, 13 Apr 2017 18:59:12:  26000000 
INFO  @ Thu, 13 Apr 2017 18:59:13:  27000000 
INFO  @ Thu, 13 Apr 2017 18:59:15:  28000000 
INFO  @ Thu, 13 Apr 2017 18:59:16:  29000000 
INFO  @ Thu, 13 Apr 2017 18:59:18:  30000000 
INFO  @ Thu, 13 Apr 2017 18:59:19:  31000000 
INFO  @ Thu, 13 Apr 2017 18:59:20:  32000000 
INFO  @ Thu, 13 Apr 2017 18:59:22:  33000000 
INFO  @ Thu, 13 Apr 2017 18:59:23:  34000000 
INFO  @ Thu, 13 Apr 2017 18:59:25:  35000000 
INFO  @ Thu, 13 Apr 2017 18:59:26:  36000000 
INFO  @ Thu, 13 Apr 2017 18:59:28:  37000000 
INFO  @ Thu, 13 Apr 2017 18:59:29:  38000000 
INFO  @ Thu, 13 Apr 2017 18:59:31:  39000000 
INFO  @ Thu, 13 Apr 2017 18:59:32:  40000000 
INFO  @ Thu, 13 Apr 2017 18:59:33:  41000000 
INFO  @ Thu, 13 Apr 2017 18:59:35:  42000000 
INFO  @ Thu, 13 Apr 2017 18:59:36:  43000000 
INFO  @ Thu, 13 Apr 2017 18:59:38:  44000000 
INFO  @ Thu, 13 Apr 2017 18:59:39:  45000000 
INFO  @ Thu, 13 Apr 2017 18:59:41:  46000000 
INFO  @ Thu, 13 Apr 2017 18:59:42:  47000000 
INFO  @ Thu, 13 Apr 2017 18:59:44:  48000000 
INFO  @ Thu, 13 Apr 2017 18:59:45:  49000000 
INFO  @ Thu, 13 Apr 2017 18:59:47:  50000000 
INFO  @ Thu, 13 Apr 2017 18:59:48:  51000000 
INFO  @ Thu, 13 Apr 2017 18:59:49:  52000000 
INFO  @ Thu, 13 Apr 2017 18:59:51:  53000000 
INFO  @ Thu, 13 Apr 2017 18:59:52:  54000000 
INFO  @ Thu, 13 Apr 2017 18:59:54:  55000000 
INFO  @ Thu, 13 Apr 2017 18:59:55:  56000000 
INFO  @ Thu, 13 Apr 2017 18:59:57:  57000000 
INFO  @ Thu, 13 Apr 2017 18:59:58:  58000000 
INFO  @ Thu, 13 Apr 2017 19:00:00:  59000000 
INFO  @ Thu, 13 Apr 2017 19:00:01:  60000000 
INFO  @ Thu, 13 Apr 2017 19:00:02:  61000000 
INFO  @ Thu, 13 Apr 2017 19:00:04:  62000000 
INFO  @ Thu, 13 Apr 2017 19:00:05:  63000000 
INFO  @ Thu, 13 Apr 2017 19:00:07:  64000000 
INFO  @ Thu, 13 Apr 2017 19:00:08:  65000000 
INFO  @ Thu, 13 Apr 2017 19:00:10:  66000000 
INFO  @ Thu, 13 Apr 2017 19:00:11:  67000000 
INFO  @ Thu, 13 Apr 2017 19:00:13:  68000000 
INFO  @ Thu, 13 Apr 2017 19:00:14:  69000000 
INFO  @ Thu, 13 Apr 2017 19:00:15:  70000000 
INFO  @ Thu, 13 Apr 2017 19:00:17:  71000000 
INFO  @ Thu, 13 Apr 2017 19:00:18:  72000000 
INFO  @ Thu, 13 Apr 2017 19:00:20:  73000000 
INFO  @ Thu, 13 Apr 2017 19:00:21:  74000000 
INFO  @ Thu, 13 Apr 2017 19:00:23:  75000000 
INFO  @ Thu, 13 Apr 2017 19:00:24:  76000000 
INFO  @ Thu, 13 Apr 2017 19:00:25:  77000000 
INFO  @ Thu, 13 Apr 2017 19:00:27:  78000000 
INFO  @ Thu, 13 Apr 2017 19:00:28:  79000000 
INFO  @ Thu, 13 Apr 2017 19:00:30:  80000000 
INFO  @ Thu, 13 Apr 2017 19:00:31:  81000000 
INFO  @ Thu, 13 Apr 2017 19:00:33:  82000000 
INFO  @ Thu, 13 Apr 2017 19:00:34:  83000000 
INFO  @ Thu, 13 Apr 2017 19:00:36:  84000000 
INFO  @ Thu, 13 Apr 2017 19:00:37:  85000000 
INFO  @ Thu, 13 Apr 2017 19:00:39:  86000000 
INFO  @ Thu, 13 Apr 2017 19:00:40:  87000000 
INFO  @ Thu, 13 Apr 2017 19:00:42:  88000000 
INFO  @ Thu, 13 Apr 2017 19:00:43:  89000000 
INFO  @ Thu, 13 Apr 2017 19:00:44:  90000000 
INFO  @ Thu, 13 Apr 2017 19:00:46:  91000000 
INFO  @ Thu, 13 Apr 2017 19:00:47:  92000000 
INFO  @ Thu, 13 Apr 2017 19:00:49:  93000000 
INFO  @ Thu, 13 Apr 2017 19:00:50:  94000000 
INFO  @ Thu, 13 Apr 2017 19:00:52:  95000000 
INFO  @ Thu, 13 Apr 2017 19:00:53:  96000000 
INFO  @ Thu, 13 Apr 2017 19:00:55:  97000000 
INFO  @ Thu, 13 Apr 2017 19:00:56:  98000000 
INFO  @ Thu, 13 Apr 2017 19:00:57:  99000000 
INFO  @ Thu, 13 Apr 2017 19:00:59: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 19:00:59: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 19:00:59: #1  total tags in treatment: 10307742 
INFO  @ Thu, 13 Apr 2017 19:00:59: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 19:00:59: #1 finished! 
INFO  @ Thu, 13 Apr 2017 19:00:59: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 19:00:59: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 19:00:59: #2 Use 225 as fragment length 
INFO  @ Thu, 13 Apr 2017 19:00:59: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 19:00:59: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 19:00:59: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:07:19: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:13:08: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:13:13: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:13:16: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:13:18: Done!

Num	10
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_19
Name	naive_overlap
Thread	thread_Root
PID	47029

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

Start	2017-04-13 19:13:32
End	2017-04-13 19:14:46
Elapsed	00:01:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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--------------------
23632 (process ID) old priority 0, new priority 19
Waiting for 40 seconds.

Num	11
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_20
Name	naive_overlap
Thread	thread_Root
PID	47030

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

Start	2017-04-13 19:13:34
End	2017-04-13 19:14:45
Elapsed	00:01:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/rep1/ENCFF888DOH.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/EGR2_MACS2/out/peak/macs2/rep2/ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_rep/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF888DOH.pr1_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF888DOH.pr2_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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--------------------
23633 (process ID) old priority 0, new priority 19
Waiting for 44 seconds.

Num	12
ID	task.report.peak2hammock.line_361.id_23
Name	peak2hammock
Thread	thread_Root
PID	27429

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

Start	2017-04-13 19:14:50
End	2017-04-13 19:15:03
Elapsed	00:00:13
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.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/EGR2_MACS2/out/peak/macs2/overlap/ENCFF888DOH_ENCFF234ALA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
27433 (process ID) old priority 0, new priority 19

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	28111

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

Start	2017-04-13 19:15:05
End	2017-04-13 19:15:13
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/EGR2_MACS2/out/report/EGR2_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/report/EGR2_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/report/EGR2_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
28115 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, EGR2_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/EGR2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep1/ENCFF888DOH.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/EGR2_MACS2/out/align/rep2/ENCFF234ALA.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/EGR2_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/EGR2_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	45524.EGR2_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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