Script file	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID	chipseq.bds.20170413_183738_690
Start time	2017-04-13 18:37:38
Run time	00:42:18.315
Tasks executed	13
Tasks failed	0
Tasks failed names
Arguments*	[-title, ZBTB17_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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_183738_690/task.callpeak_macs2.macs2_g_b_pooled_rep.line_155.id_10 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_ppr1.line_155.id_11 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_ppr2.line_155.id_12 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_rep1.line_155.id_13 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_rep1_pr1.line_155.id_14 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_rep1_pr2.line_155.id_15 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_rep2.line_155.id_16 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_rep2_pr1.line_155.id_17 chipseq.bds.20170413_183738_690/task.callpeak_macs2.macs2_g_b_rep2_pr2.line_155.id_18 chipseq.bds.20170413_183738_690/task.callpeak_naive_overlap.naive_overlap.line_143.id_19 chipseq.bds.20170413_183738_690/task.callpeak_naive_overlap.naive_overlap.line_143.id_20 chipseq.bds.20170413_183738_690/task.report.peak2hammock.line_361.id_23 chipseq.bds.20170413_183738_690/task.graphviz.report.line_97.id_24
thread_42	thread_Root
thread_43	thread_Root
thread_41	thread_Root

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.callpeak_macs2.macs2_g_b_pooled_rep.line_155.id_10
Name	macs2 g/b pooled_rep
Thread	thread_Root
PID	46970

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

Start	2017-04-13 18:37:52
End	2017-04-13 19:08:09
Elapsed	00:30:17
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.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--------------------
14458 (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/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_rep/ENCFF057NJA_ENCFF078YAS.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 18:38:34:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:38:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:40:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:15:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:36:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:49:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:55:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  51000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  52000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  53000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  54000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  55000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  56000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  57000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  58000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:22:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:28:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:43:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  72000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  73000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  74000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  75000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  77000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  78000000 
INFO  @ Thu, 13 Apr 2017 18:41:02:  79000000 
INFO  @ Thu, 13 Apr 2017 18:41:04:  80000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  81000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  82000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  83000000 
INFO  @ Thu, 13 Apr 2017 18:41:12:  84000000 
INFO  @ Thu, 13 Apr 2017 18:41:14:  85000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  86000000 
INFO  @ Thu, 13 Apr 2017 18:41:18:  87000000 
INFO  @ Thu, 13 Apr 2017 18:41:20:  88000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  89000000 
INFO  @ Thu, 13 Apr 2017 18:41:24:  90000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  91000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  92000000 
INFO  @ Thu, 13 Apr 2017 18:41:31:  93000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  94000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  95000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  96000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  97000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  98000000 
INFO  @ Thu, 13 Apr 2017 18:41:43:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  100000000 
INFO  @ Thu, 13 Apr 2017 18:41:48:  101000000 
INFO  @ Thu, 13 Apr 2017 18:41:50:  102000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  103000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  104000000 
INFO  @ Thu, 13 Apr 2017 18:41:56:  105000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  106000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  107000000 
INFO  @ Thu, 13 Apr 2017 18:42:03:  108000000 
INFO  @ Thu, 13 Apr 2017 18:42:05:  109000000 
INFO  @ Thu, 13 Apr 2017 18:42:07:  110000000 
INFO  @ Thu, 13 Apr 2017 18:42:09:  111000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  112000000 
INFO  @ Thu, 13 Apr 2017 18:42:13:  113000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  114000000 
INFO  @ Thu, 13 Apr 2017 18:42:17:  115000000 
INFO  @ Thu, 13 Apr 2017 18:42:29: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:42:31:  1000000 
INFO  @ Thu, 13 Apr 2017 18:42:33:  2000000 
INFO  @ Thu, 13 Apr 2017 18:42:35:  3000000 
INFO  @ Thu, 13 Apr 2017 18:42:37:  4000000 
INFO  @ Thu, 13 Apr 2017 18:42:39:  5000000 
INFO  @ Thu, 13 Apr 2017 18:42:41:  6000000 
INFO  @ Thu, 13 Apr 2017 18:42:43:  7000000 
INFO  @ Thu, 13 Apr 2017 18:42:45:  8000000 
INFO  @ Thu, 13 Apr 2017 18:42:47:  9000000 
INFO  @ Thu, 13 Apr 2017 18:42:49:  10000000 
INFO  @ Thu, 13 Apr 2017 18:42:51:  11000000 
INFO  @ Thu, 13 Apr 2017 18:42:53:  12000000 
INFO  @ Thu, 13 Apr 2017 18:42:55:  13000000 
INFO  @ Thu, 13 Apr 2017 18:42:57:  14000000 
INFO  @ Thu, 13 Apr 2017 18:42:59:  15000000 
INFO  @ Thu, 13 Apr 2017 18:43:01:  16000000 
INFO  @ Thu, 13 Apr 2017 18:43:03:  17000000 
INFO  @ Thu, 13 Apr 2017 18:43:05:  18000000 
INFO  @ Thu, 13 Apr 2017 18:43:07:  19000000 
INFO  @ Thu, 13 Apr 2017 18:43:09:  20000000 
INFO  @ Thu, 13 Apr 2017 18:43:11:  21000000 
INFO  @ Thu, 13 Apr 2017 18:43:13:  22000000 
INFO  @ Thu, 13 Apr 2017 18:43:15:  23000000 
INFO  @ Thu, 13 Apr 2017 18:43:17:  24000000 
INFO  @ Thu, 13 Apr 2017 18:43:19:  25000000 
INFO  @ Thu, 13 Apr 2017 18:43:21:  26000000 
INFO  @ Thu, 13 Apr 2017 18:43:22:  27000000 
INFO  @ Thu, 13 Apr 2017 18:43:24:  28000000 
INFO  @ Thu, 13 Apr 2017 18:43:26:  29000000 
INFO  @ Thu, 13 Apr 2017 18:43:28:  30000000 
INFO  @ Thu, 13 Apr 2017 18:43:30:  31000000 
INFO  @ Thu, 13 Apr 2017 18:43:32:  32000000 
INFO  @ Thu, 13 Apr 2017 18:43:34:  33000000 
INFO  @ Thu, 13 Apr 2017 18:43:36:  34000000 
INFO  @ Thu, 13 Apr 2017 18:43:37:  35000000 
INFO  @ Thu, 13 Apr 2017 18:43:39:  36000000 
INFO  @ Thu, 13 Apr 2017 18:43:41:  37000000 
INFO  @ Thu, 13 Apr 2017 18:43:43:  38000000 
INFO  @ Thu, 13 Apr 2017 18:43:45:  39000000 
INFO  @ Thu, 13 Apr 2017 18:43:47:  40000000 
INFO  @ Thu, 13 Apr 2017 18:43:49:  41000000 
INFO  @ Thu, 13 Apr 2017 18:43:51:  42000000 
INFO  @ Thu, 13 Apr 2017 18:43:53:  43000000 
INFO  @ Thu, 13 Apr 2017 18:43:55:  44000000 
INFO  @ Thu, 13 Apr 2017 18:43:57:  45000000 
INFO  @ Thu, 13 Apr 2017 18:43:59:  46000000 
INFO  @ Thu, 13 Apr 2017 18:44:01:  47000000 
INFO  @ Thu, 13 Apr 2017 18:44:03:  48000000 
INFO  @ Thu, 13 Apr 2017 18:44:05:  49000000 
INFO  @ Thu, 13 Apr 2017 18:44:07:  50000000 
INFO  @ Thu, 13 Apr 2017 18:44:09:  51000000 
INFO  @ Thu, 13 Apr 2017 18:44:11:  52000000 
INFO  @ Thu, 13 Apr 2017 18:44:13:  53000000 
INFO  @ Thu, 13 Apr 2017 18:44:15:  54000000 
INFO  @ Thu, 13 Apr 2017 18:44:17:  55000000 
INFO  @ Thu, 13 Apr 2017 18:44:19:  56000000 
INFO  @ Thu, 13 Apr 2017 18:44:21:  57000000 
INFO  @ Thu, 13 Apr 2017 18:44:23:  58000000 
INFO  @ Thu, 13 Apr 2017 18:44:25:  59000000 
INFO  @ Thu, 13 Apr 2017 18:44:27:  60000000 
INFO  @ Thu, 13 Apr 2017 18:44:29:  61000000 
INFO  @ Thu, 13 Apr 2017 18:44:31:  62000000 
INFO  @ Thu, 13 Apr 2017 18:44:32:  63000000 
INFO  @ Thu, 13 Apr 2017 18:44:34:  64000000 
INFO  @ Thu, 13 Apr 2017 18:44:36:  65000000 
INFO  @ Thu, 13 Apr 2017 18:44:38:  66000000 
INFO  @ Thu, 13 Apr 2017 18:44:40:  67000000 
INFO  @ Thu, 13 Apr 2017 18:44:42:  68000000 
INFO  @ Thu, 13 Apr 2017 18:44:44:  69000000 
INFO  @ Thu, 13 Apr 2017 18:44:46:  70000000 
INFO  @ Thu, 13 Apr 2017 18:44:48:  71000000 
INFO  @ Thu, 13 Apr 2017 18:44:50:  72000000 
INFO  @ Thu, 13 Apr 2017 18:44:52:  73000000 
INFO  @ Thu, 13 Apr 2017 18:44:54:  74000000 
INFO  @ Thu, 13 Apr 2017 18:44:56:  75000000 
INFO  @ Thu, 13 Apr 2017 18:44:58:  76000000 
INFO  @ Thu, 13 Apr 2017 18:45:00:  77000000 
INFO  @ Thu, 13 Apr 2017 18:45:02:  78000000 
INFO  @ Thu, 13 Apr 2017 18:45:04:  79000000 
INFO  @ Thu, 13 Apr 2017 18:45:05:  80000000 
INFO  @ Thu, 13 Apr 2017 18:45:07:  81000000 
INFO  @ Thu, 13 Apr 2017 18:45:09:  82000000 
INFO  @ Thu, 13 Apr 2017 18:45:11:  83000000 
INFO  @ Thu, 13 Apr 2017 18:45:13:  84000000 
INFO  @ Thu, 13 Apr 2017 18:45:15:  85000000 
INFO  @ Thu, 13 Apr 2017 18:45:17:  86000000 
INFO  @ Thu, 13 Apr 2017 18:45:19:  87000000 
INFO  @ Thu, 13 Apr 2017 18:45:21:  88000000 
INFO  @ Thu, 13 Apr 2017 18:45:23:  89000000 
INFO  @ Thu, 13 Apr 2017 18:45:25:  90000000 
INFO  @ Thu, 13 Apr 2017 18:45:26:  91000000 
INFO  @ Thu, 13 Apr 2017 18:45:28:  92000000 
INFO  @ Thu, 13 Apr 2017 18:45:30:  93000000 
INFO  @ Thu, 13 Apr 2017 18:45:32:  94000000 
INFO  @ Thu, 13 Apr 2017 18:45:34:  95000000 
INFO  @ Thu, 13 Apr 2017 18:45:36:  96000000 
INFO  @ Thu, 13 Apr 2017 18:45:38:  97000000 
INFO  @ Thu, 13 Apr 2017 18:45:40:  98000000 
INFO  @ Thu, 13 Apr 2017 18:45:41:  99000000 
INFO  @ Thu, 13 Apr 2017 18:45:43: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:45:43: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:45:43: #1  total tags in treatment: 115595584 
INFO  @ Thu, 13 Apr 2017 18:45:43: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:45:43: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:45:43: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:45:43: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:45:43: #2 Use 255 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:45:43: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:45:43: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:45:43: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:57:44: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:08:01: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:08:02: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:08:04: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:08:04: Done!

Num	2
ID	task.callpeak_macs2.macs2_g_b_ppr1.line_155.id_11
Name	macs2 g/b ppr1
Thread	thread_Root
PID	46977

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

Start	2017-04-13 18:37:55
End	2017-04-13 18:53:14
Elapsed	00:15:19
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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--------------------
48792 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:17:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:19:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:24:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:27:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:30:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:32:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  25000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:01:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  56000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  57000000 
INFO  @ Thu, 13 Apr 2017 18:39:53: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:39:55:  1000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  2000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  3000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  4000000 
INFO  @ Thu, 13 Apr 2017 18:40:01:  5000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  6000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  7000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  8000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  9000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  10000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  11000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  12000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  13000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  14000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  15000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  16000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  17000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  18000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  19000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  20000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  21000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  22000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  23000000 
INFO  @ Thu, 13 Apr 2017 18:40:28:  24000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  25000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  26000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  27000000 
INFO  @ Thu, 13 Apr 2017 18:40:34:  28000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  29000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  30000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  31000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  32000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  33000000 
INFO  @ Thu, 13 Apr 2017 18:40:43:  34000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  35000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  36000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  37000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  38000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  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 18:40:56:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:59:  45000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  46000000 
INFO  @ Thu, 13 Apr 2017 18:41:02:  47000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  48000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  49000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  50000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  51000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  52000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  53000000 
INFO  @ Thu, 13 Apr 2017 18:41:12:  54000000 
INFO  @ Thu, 13 Apr 2017 18:41:14:  55000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  56000000 
INFO  @ Thu, 13 Apr 2017 18:41:17:  57000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  58000000 
INFO  @ Thu, 13 Apr 2017 18:41:20:  59000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  60000000 
INFO  @ Thu, 13 Apr 2017 18:41:23:  61000000 
INFO  @ Thu, 13 Apr 2017 18:41:25:  62000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  63000000 
INFO  @ Thu, 13 Apr 2017 18:41:27:  64000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  65000000 
INFO  @ Thu, 13 Apr 2017 18:41:30:  66000000 
INFO  @ Thu, 13 Apr 2017 18:41:31:  67000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  68000000 
INFO  @ Thu, 13 Apr 2017 18:41:34:  69000000 
INFO  @ Thu, 13 Apr 2017 18:41:36:  70000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  71000000 
INFO  @ Thu, 13 Apr 2017 18:41:38:  72000000 
INFO  @ Thu, 13 Apr 2017 18:41:40:  73000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  74000000 
INFO  @ Thu, 13 Apr 2017 18:41:43:  75000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  76000000 
INFO  @ Thu, 13 Apr 2017 18:41:46:  77000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  78000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  79000000 
INFO  @ Thu, 13 Apr 2017 18:41:51:  80000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  81000000 
INFO  @ Thu, 13 Apr 2017 18:41:53:  82000000 
INFO  @ Thu, 13 Apr 2017 18:41:55:  83000000 
INFO  @ Thu, 13 Apr 2017 18:41:57:  84000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  85000000 
INFO  @ Thu, 13 Apr 2017 18:41:59:  86000000 
INFO  @ Thu, 13 Apr 2017 18:42:01:  87000000 
INFO  @ Thu, 13 Apr 2017 18:42:02:  88000000 
INFO  @ Thu, 13 Apr 2017 18:42:03:  89000000 
INFO  @ Thu, 13 Apr 2017 18:42:05:  90000000 
INFO  @ Thu, 13 Apr 2017 18:42:06:  91000000 
INFO  @ Thu, 13 Apr 2017 18:42:08:  92000000 
INFO  @ Thu, 13 Apr 2017 18:42:09:  93000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  94000000 
INFO  @ Thu, 13 Apr 2017 18:42:12:  95000000 
INFO  @ Thu, 13 Apr 2017 18:42:13:  96000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  97000000 
INFO  @ Thu, 13 Apr 2017 18:42:16:  98000000 
INFO  @ Thu, 13 Apr 2017 18:42:18:  99000000 
INFO  @ Thu, 13 Apr 2017 18:42:20: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:42:20: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:42:20: #1  total tags in treatment: 57797794 
INFO  @ Thu, 13 Apr 2017 18:42:20: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:42:20: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:42:20: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:42:20: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:42:20: #2 Use 255 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:42:20: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:42:20: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:42:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:48:03: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:53:09: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:53:10: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:53:10: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:53:11: Done!

Num	3
ID	task.callpeak_macs2.macs2_g_b_ppr2.line_155.id_12
Name	macs2 g/b ppr2
Thread	thread_Root
PID	46979

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

Start	2017-04-13 18:37:56
End	2017-04-13 18:53:31
Elapsed	00:15:35
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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--------------------
48791 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:38:16: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 255 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:16: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:18:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:21:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:30:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:33:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:36:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:38:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:43:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:49:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  23000000 
INFO  @ Thu, 13 Apr 2017 18:38:55:  24000000 
INFO  @ Thu, 13 Apr 2017 18:38:57:  25000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:05:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:11:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:24:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:30:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  48000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  49000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  50000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  51000000 
INFO  @ Thu, 13 Apr 2017 18:39:40:  52000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  53000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  54000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  55000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  56000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  57000000 
INFO  @ Thu, 13 Apr 2017 18:39:53: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:39:55:  1000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  2000000 
INFO  @ Thu, 13 Apr 2017 18:39:58:  3000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  4000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  5000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  6000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  7000000 
INFO  @ Thu, 13 Apr 2017 18:40:05:  8000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  9000000 
INFO  @ Thu, 13 Apr 2017 18:40:08:  10000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  11000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  12000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  13000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  14000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  15000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  16000000 
INFO  @ Thu, 13 Apr 2017 18:40:18:  17000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  18000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  19000000 
INFO  @ Thu, 13 Apr 2017 18:40:22:  20000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  21000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  22000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  23000000 
INFO  @ Thu, 13 Apr 2017 18:40:28:  24000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  25000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  26000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  27000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  28000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  29000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  30000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  31000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  32000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  33000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  34000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  35000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  36000000 
INFO  @ Thu, 13 Apr 2017 18:40:47:  37000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  38000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  39000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  40000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  41000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  42000000 
INFO  @ Thu, 13 Apr 2017 18:40:55:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  45000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  46000000 
INFO  @ Thu, 13 Apr 2017 18:41:01:  47000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  48000000 
INFO  @ Thu, 13 Apr 2017 18:41:04:  49000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  50000000 
INFO  @ Thu, 13 Apr 2017 18:41:07:  51000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  52000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  53000000 
INFO  @ Thu, 13 Apr 2017 18:41:12:  54000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  55000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  56000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  57000000 
INFO  @ Thu, 13 Apr 2017 18:41:17:  58000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  59000000 
INFO  @ Thu, 13 Apr 2017 18:41:20:  60000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  61000000 
INFO  @ Thu, 13 Apr 2017 18:41:23:  62000000 
INFO  @ Thu, 13 Apr 2017 18:41:25:  63000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  64000000 
INFO  @ Thu, 13 Apr 2017 18:41:27:  65000000 
INFO  @ Thu, 13 Apr 2017 18:41:29:  66000000 
INFO  @ Thu, 13 Apr 2017 18:41:30:  67000000 
INFO  @ Thu, 13 Apr 2017 18:41:32:  68000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  69000000 
INFO  @ Thu, 13 Apr 2017 18:41:34:  70000000 
INFO  @ Thu, 13 Apr 2017 18:41:36:  71000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  72000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  73000000 
INFO  @ Thu, 13 Apr 2017 18:41:40:  74000000 
INFO  @ Thu, 13 Apr 2017 18:41:42:  75000000 
INFO  @ Thu, 13 Apr 2017 18:41:43:  76000000 
INFO  @ Thu, 13 Apr 2017 18:41:44:  77000000 
INFO  @ Thu, 13 Apr 2017 18:41:46:  78000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  79000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  80000000 
INFO  @ Thu, 13 Apr 2017 18:41:50:  81000000 
INFO  @ Thu, 13 Apr 2017 18:41:51:  82000000 
INFO  @ Thu, 13 Apr 2017 18:41:53:  83000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  84000000 
INFO  @ Thu, 13 Apr 2017 18:41:56:  85000000 
INFO  @ Thu, 13 Apr 2017 18:41:57:  86000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  87000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  88000000 
INFO  @ Thu, 13 Apr 2017 18:42:02:  89000000 
INFO  @ Thu, 13 Apr 2017 18:42:03:  90000000 
INFO  @ Thu, 13 Apr 2017 18:42:05:  91000000 
INFO  @ Thu, 13 Apr 2017 18:42:06:  92000000 
INFO  @ Thu, 13 Apr 2017 18:42:08:  93000000 
INFO  @ Thu, 13 Apr 2017 18:42:09:  94000000 
INFO  @ Thu, 13 Apr 2017 18:42:11:  95000000 
INFO  @ Thu, 13 Apr 2017 18:42:12:  96000000 
INFO  @ Thu, 13 Apr 2017 18:42:14:  97000000 
INFO  @ Thu, 13 Apr 2017 18:42:15:  98000000 
INFO  @ Thu, 13 Apr 2017 18:42:17:  99000000 
INFO  @ Thu, 13 Apr 2017 18:42:18: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:42:18: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:42:18: #1  total tags in treatment: 57797790 
INFO  @ Thu, 13 Apr 2017 18:42:18: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:42:18: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:42:18: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:42:18: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:42:18: #2 Use 255 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:42:18: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:42:18: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:42:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:48:15: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:53:25: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:53:26: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:53:27: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:53:27: Done!

Num	4
ID	task.callpeak_macs2.macs2_g_b_rep1.line_155.id_13
Name	macs2 g/b rep1
Thread	thread_Root
PID	46985

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

Start	2017-04-13 18:37:58
End	2017-04-13 18:57:54
Elapsed	00:19:56
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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--------------------
14459 (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/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.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 18:38:42:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:46:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:52:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:54:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:56:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:58:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:00:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:08:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:21:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:27:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:33:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:43:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:46:  43000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  44000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  45000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  46000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  47000000 
INFO  @ Thu, 13 Apr 2017 18:39:58: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:40:00:  1000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  2000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  3000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  4000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  5000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  6000000 
INFO  @ Thu, 13 Apr 2017 18:40:11:  7000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  8000000 
INFO  @ Thu, 13 Apr 2017 18:40:15:  9000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  10000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  11000000 
INFO  @ Thu, 13 Apr 2017 18:40:21:  12000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  13000000 
INFO  @ Thu, 13 Apr 2017 18:40:25:  14000000 
INFO  @ Thu, 13 Apr 2017 18:40:27:  15000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  16000000 
INFO  @ Thu, 13 Apr 2017 18:40:31:  17000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  18000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  19000000 
INFO  @ Thu, 13 Apr 2017 18:40:37:  20000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  21000000 
INFO  @ Thu, 13 Apr 2017 18:40:40:  22000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  23000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  24000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  25000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  26000000 
INFO  @ Thu, 13 Apr 2017 18:40:50:  27000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  28000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  29000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  30000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  31000000 
INFO  @ Thu, 13 Apr 2017 18:40:59:  32000000 
INFO  @ Thu, 13 Apr 2017 18:41:01:  33000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  34000000 
INFO  @ Thu, 13 Apr 2017 18:41:05:  35000000 
INFO  @ Thu, 13 Apr 2017 18:41:07:  36000000 
INFO  @ Thu, 13 Apr 2017 18:41:09:  37000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  38000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  39000000 
INFO  @ Thu, 13 Apr 2017 18:41:15:  40000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  41000000 
INFO  @ Thu, 13 Apr 2017 18:41:18:  42000000 
INFO  @ Thu, 13 Apr 2017 18:41:20:  43000000 
INFO  @ Thu, 13 Apr 2017 18:41:22:  44000000 
INFO  @ Thu, 13 Apr 2017 18:41:24:  45000000 
INFO  @ Thu, 13 Apr 2017 18:41:26:  46000000 
INFO  @ Thu, 13 Apr 2017 18:41:28:  47000000 
INFO  @ Thu, 13 Apr 2017 18:41:30:  48000000 
INFO  @ Thu, 13 Apr 2017 18:41:31:  49000000 
INFO  @ Thu, 13 Apr 2017 18:41:33:  50000000 
INFO  @ Thu, 13 Apr 2017 18:41:35:  51000000 
INFO  @ Thu, 13 Apr 2017 18:41:37:  52000000 
INFO  @ Thu, 13 Apr 2017 18:41:39:  53000000 
INFO  @ Thu, 13 Apr 2017 18:41:41:  54000000 
INFO  @ Thu, 13 Apr 2017 18:41:43:  55000000 
INFO  @ Thu, 13 Apr 2017 18:41:45:  56000000 
INFO  @ Thu, 13 Apr 2017 18:41:47:  57000000 
INFO  @ Thu, 13 Apr 2017 18:41:49:  58000000 
INFO  @ Thu, 13 Apr 2017 18:41:50:  59000000 
INFO  @ Thu, 13 Apr 2017 18:41:52:  60000000 
INFO  @ Thu, 13 Apr 2017 18:41:54:  61000000 
INFO  @ Thu, 13 Apr 2017 18:41:56:  62000000 
INFO  @ Thu, 13 Apr 2017 18:41:58:  63000000 
INFO  @ Thu, 13 Apr 2017 18:42:00:  64000000 
INFO  @ Thu, 13 Apr 2017 18:42:02:  65000000 
INFO  @ Thu, 13 Apr 2017 18:42:04:  66000000 
INFO  @ Thu, 13 Apr 2017 18:42:06:  67000000 
INFO  @ Thu, 13 Apr 2017 18:42:08:  68000000 
INFO  @ Thu, 13 Apr 2017 18:42:10:  69000000 
INFO  @ Thu, 13 Apr 2017 18:42:12:  70000000 
INFO  @ Thu, 13 Apr 2017 18:42:14:  71000000 
INFO  @ Thu, 13 Apr 2017 18:42:16:  72000000 
INFO  @ Thu, 13 Apr 2017 18:42:17:  73000000 
INFO  @ Thu, 13 Apr 2017 18:42:19:  74000000 
INFO  @ Thu, 13 Apr 2017 18:42:21:  75000000 
INFO  @ Thu, 13 Apr 2017 18:42:23:  76000000 
INFO  @ Thu, 13 Apr 2017 18:42:25:  77000000 
INFO  @ Thu, 13 Apr 2017 18:42:27:  78000000 
INFO  @ Thu, 13 Apr 2017 18:42:29:  79000000 
INFO  @ Thu, 13 Apr 2017 18:42:31:  80000000 
INFO  @ Thu, 13 Apr 2017 18:42:33:  81000000 
INFO  @ Thu, 13 Apr 2017 18:42:35:  82000000 
INFO  @ Thu, 13 Apr 2017 18:42:37:  83000000 
INFO  @ Thu, 13 Apr 2017 18:42:39:  84000000 
INFO  @ Thu, 13 Apr 2017 18:42:41:  85000000 
INFO  @ Thu, 13 Apr 2017 18:42:42:  86000000 
INFO  @ Thu, 13 Apr 2017 18:42:45:  87000000 
INFO  @ Thu, 13 Apr 2017 18:42:46:  88000000 
INFO  @ Thu, 13 Apr 2017 18:42:48:  89000000 
INFO  @ Thu, 13 Apr 2017 18:42:50:  90000000 
INFO  @ Thu, 13 Apr 2017 18:42:52:  91000000 
INFO  @ Thu, 13 Apr 2017 18:42:54:  92000000 
INFO  @ Thu, 13 Apr 2017 18:42:56:  93000000 
INFO  @ Thu, 13 Apr 2017 18:42:58:  94000000 
INFO  @ Thu, 13 Apr 2017 18:43:00:  95000000 
INFO  @ Thu, 13 Apr 2017 18:43:02:  96000000 
INFO  @ Thu, 13 Apr 2017 18:43:04:  97000000 
INFO  @ Thu, 13 Apr 2017 18:43:05:  98000000 
INFO  @ Thu, 13 Apr 2017 18:43:07:  99000000 
INFO  @ Thu, 13 Apr 2017 18:43:09: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:43:09: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:43:09: #1  total tags in treatment: 47187626 
INFO  @ Thu, 13 Apr 2017 18:43:09: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:43:09: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:43:09: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:43:09: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:43:09: #2 Use 265 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:43:09: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:43:09: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:43:09: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:50:35: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:57:44: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:57:46: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:57:48: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:57:49: 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	46993

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

Start	2017-04-13 18:38:02
End	2017-04-13 18:51:09
Elapsed	00:13:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.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--------------------
24532 (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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz']
# control file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is on
 
INFO  @ Thu, 13 Apr 2017 18:38:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:38:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:38:19:  1000000 
INFO  @ Thu, 13 Apr 2017 18:38:20:  2000000 
INFO  @ Thu, 13 Apr 2017 18:38:22:  3000000 
INFO  @ Thu, 13 Apr 2017 18:38:23:  4000000 
INFO  @ Thu, 13 Apr 2017 18:38:25:  5000000 
INFO  @ Thu, 13 Apr 2017 18:38:26:  6000000 
INFO  @ Thu, 13 Apr 2017 18:38:28:  7000000 
INFO  @ Thu, 13 Apr 2017 18:38:29:  8000000 
INFO  @ Thu, 13 Apr 2017 18:38:31:  9000000 
INFO  @ Thu, 13 Apr 2017 18:38:32:  10000000 
INFO  @ Thu, 13 Apr 2017 18:38:34:  11000000 
INFO  @ Thu, 13 Apr 2017 18:38:35:  12000000 
INFO  @ Thu, 13 Apr 2017 18:38:37:  13000000 
INFO  @ Thu, 13 Apr 2017 18:38:39:  14000000 
INFO  @ Thu, 13 Apr 2017 18:38:41:  15000000 
INFO  @ Thu, 13 Apr 2017 18:38:42:  16000000 
INFO  @ Thu, 13 Apr 2017 18:38:44:  17000000 
INFO  @ Thu, 13 Apr 2017 18:38:45:  18000000 
INFO  @ Thu, 13 Apr 2017 18:38:47:  19000000 
INFO  @ Thu, 13 Apr 2017 18:38:48:  20000000 
INFO  @ Thu, 13 Apr 2017 18:38:50:  21000000 
INFO  @ Thu, 13 Apr 2017 18:38:51:  22000000 
INFO  @ Thu, 13 Apr 2017 18:38:53:  23000000 
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 18:39:00:  3000000 
INFO  @ Thu, 13 Apr 2017 18:39:02:  4000000 
INFO  @ Thu, 13 Apr 2017 18:39:03:  5000000 
INFO  @ Thu, 13 Apr 2017 18:39:04:  6000000 
INFO  @ Thu, 13 Apr 2017 18:39:06:  7000000 
INFO  @ Thu, 13 Apr 2017 18:39:07:  8000000 
INFO  @ Thu, 13 Apr 2017 18:39:09:  9000000 
INFO  @ Thu, 13 Apr 2017 18:39:10:  10000000 
INFO  @ Thu, 13 Apr 2017 18:39:12:  11000000 
INFO  @ Thu, 13 Apr 2017 18:39:13:  12000000 
INFO  @ Thu, 13 Apr 2017 18:39:14:  13000000 
INFO  @ Thu, 13 Apr 2017 18:39:16:  14000000 
INFO  @ Thu, 13 Apr 2017 18:39:17:  15000000 
INFO  @ Thu, 13 Apr 2017 18:39:19:  16000000 
INFO  @ Thu, 13 Apr 2017 18:39:20:  17000000 
INFO  @ Thu, 13 Apr 2017 18:39:22:  18000000 
INFO  @ Thu, 13 Apr 2017 18:39:23:  19000000 
INFO  @ Thu, 13 Apr 2017 18:39:25:  20000000 
INFO  @ Thu, 13 Apr 2017 18:39:26:  21000000 
INFO  @ Thu, 13 Apr 2017 18:39:28:  22000000 
INFO  @ Thu, 13 Apr 2017 18:39:29:  23000000 
INFO  @ Thu, 13 Apr 2017 18:39:31:  24000000 
INFO  @ Thu, 13 Apr 2017 18:39:32:  25000000 
INFO  @ Thu, 13 Apr 2017 18:39:34:  26000000 
INFO  @ Thu, 13 Apr 2017 18:39:35:  27000000 
INFO  @ Thu, 13 Apr 2017 18:39:37:  28000000 
INFO  @ Thu, 13 Apr 2017 18:39:38:  29000000 
INFO  @ Thu, 13 Apr 2017 18:39:39:  30000000 
INFO  @ Thu, 13 Apr 2017 18:39:41:  31000000 
INFO  @ Thu, 13 Apr 2017 18:39:42:  32000000 
INFO  @ Thu, 13 Apr 2017 18:39:44:  33000000 
INFO  @ Thu, 13 Apr 2017 18:39:45:  34000000 
INFO  @ Thu, 13 Apr 2017 18:39:47:  35000000 
INFO  @ Thu, 13 Apr 2017 18:39:48:  36000000 
INFO  @ Thu, 13 Apr 2017 18:39:50:  37000000 
INFO  @ Thu, 13 Apr 2017 18:39:51:  38000000 
INFO  @ Thu, 13 Apr 2017 18:39:53:  39000000 
INFO  @ Thu, 13 Apr 2017 18:39:54:  40000000 
INFO  @ Thu, 13 Apr 2017 18:39:56:  41000000 
INFO  @ Thu, 13 Apr 2017 18:39:57:  42000000 
INFO  @ Thu, 13 Apr 2017 18:39:59:  43000000 
INFO  @ Thu, 13 Apr 2017 18:40:00:  44000000 
INFO  @ Thu, 13 Apr 2017 18:40:02:  45000000 
INFO  @ Thu, 13 Apr 2017 18:40:03:  46000000 
INFO  @ Thu, 13 Apr 2017 18:40:04:  47000000 
INFO  @ Thu, 13 Apr 2017 18:40:06:  48000000 
INFO  @ Thu, 13 Apr 2017 18:40:07:  49000000 
INFO  @ Thu, 13 Apr 2017 18:40:09:  50000000 
INFO  @ Thu, 13 Apr 2017 18:40:10:  51000000 
INFO  @ Thu, 13 Apr 2017 18:40:12:  52000000 
INFO  @ Thu, 13 Apr 2017 18:40:13:  53000000 
INFO  @ Thu, 13 Apr 2017 18:40:14:  54000000 
INFO  @ Thu, 13 Apr 2017 18:40:16:  55000000 
INFO  @ Thu, 13 Apr 2017 18:40:17:  56000000 
INFO  @ Thu, 13 Apr 2017 18:40:19:  57000000 
INFO  @ Thu, 13 Apr 2017 18:40:20:  58000000 
INFO  @ Thu, 13 Apr 2017 18:40:22:  59000000 
INFO  @ Thu, 13 Apr 2017 18:40:23:  60000000 
INFO  @ Thu, 13 Apr 2017 18:40:24:  61000000 
INFO  @ Thu, 13 Apr 2017 18:40:26:  62000000 
INFO  @ Thu, 13 Apr 2017 18:40:28:  63000000 
INFO  @ Thu, 13 Apr 2017 18:40:29:  64000000 
INFO  @ Thu, 13 Apr 2017 18:40:30:  65000000 
INFO  @ Thu, 13 Apr 2017 18:40:32:  66000000 
INFO  @ Thu, 13 Apr 2017 18:40:33:  67000000 
INFO  @ Thu, 13 Apr 2017 18:40:35:  68000000 
INFO  @ Thu, 13 Apr 2017 18:40:36:  69000000 
INFO  @ Thu, 13 Apr 2017 18:40:38:  70000000 
INFO  @ Thu, 13 Apr 2017 18:40:39:  71000000 
INFO  @ Thu, 13 Apr 2017 18:40:41:  72000000 
INFO  @ Thu, 13 Apr 2017 18:40:42:  73000000 
INFO  @ Thu, 13 Apr 2017 18:40:44:  74000000 
INFO  @ Thu, 13 Apr 2017 18:40:45:  75000000 
INFO  @ Thu, 13 Apr 2017 18:40:46:  76000000 
INFO  @ Thu, 13 Apr 2017 18:40:48:  77000000 
INFO  @ Thu, 13 Apr 2017 18:40:49:  78000000 
INFO  @ Thu, 13 Apr 2017 18:40:51:  79000000 
INFO  @ Thu, 13 Apr 2017 18:40:52:  80000000 
INFO  @ Thu, 13 Apr 2017 18:40:54:  81000000 
INFO  @ Thu, 13 Apr 2017 18:40:56:  82000000 
INFO  @ Thu, 13 Apr 2017 18:40:57:  83000000 
INFO  @ Thu, 13 Apr 2017 18:40:58:  84000000 
INFO  @ Thu, 13 Apr 2017 18:41:00:  85000000 
INFO  @ Thu, 13 Apr 2017 18:41:01:  86000000 
INFO  @ Thu, 13 Apr 2017 18:41:03:  87000000 
INFO  @ Thu, 13 Apr 2017 18:41:04:  88000000 
INFO  @ Thu, 13 Apr 2017 18:41:06:  89000000 
INFO  @ Thu, 13 Apr 2017 18:41:07:  90000000 
INFO  @ Thu, 13 Apr 2017 18:41:08:  91000000 
INFO  @ Thu, 13 Apr 2017 18:41:10:  92000000 
INFO  @ Thu, 13 Apr 2017 18:41:11:  93000000 
INFO  @ Thu, 13 Apr 2017 18:41:13:  94000000 
INFO  @ Thu, 13 Apr 2017 18:41:14:  95000000 
INFO  @ Thu, 13 Apr 2017 18:41:16:  96000000 
INFO  @ Thu, 13 Apr 2017 18:41:17:  97000000 
INFO  @ Thu, 13 Apr 2017 18:41:19:  98000000 
INFO  @ Thu, 13 Apr 2017 18:41:20:  99000000 
INFO  @ Thu, 13 Apr 2017 18:41:22: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:41:22: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:41:22: #1  total tags in treatment: 23593814 
INFO  @ Thu, 13 Apr 2017 18:41:22: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:41:22: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:41:22: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:41:22: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:41:22: #2 Use 265 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:41:22: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:41:22: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:41:22: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:46:32: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 18:50:56: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 18:50:59: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 18:51:01: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 18:51:04: 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	47015

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

Start	2017-04-13 18:51:13
End	2017-04-13 19:03:54
Elapsed	00:12:40
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.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--------------------
24030 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:51:31: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 265 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF057NJA.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 18:51:31: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:51:31: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:51:32:  1000000 
INFO  @ Thu, 13 Apr 2017 18:51:34:  2000000 
INFO  @ Thu, 13 Apr 2017 18:51:35:  3000000 
INFO  @ Thu, 13 Apr 2017 18:51:37:  4000000 
INFO  @ Thu, 13 Apr 2017 18:51:38:  5000000 
INFO  @ Thu, 13 Apr 2017 18:51:40:  6000000 
INFO  @ Thu, 13 Apr 2017 18:51:41:  7000000 
INFO  @ Thu, 13 Apr 2017 18:51:43:  8000000 
INFO  @ Thu, 13 Apr 2017 18:51:45:  9000000 
INFO  @ Thu, 13 Apr 2017 18:51:46:  10000000 
INFO  @ Thu, 13 Apr 2017 18:51:48:  11000000 
INFO  @ Thu, 13 Apr 2017 18:51:49:  12000000 
INFO  @ Thu, 13 Apr 2017 18:51:51:  13000000 
INFO  @ Thu, 13 Apr 2017 18:51:52:  14000000 
INFO  @ Thu, 13 Apr 2017 18:51:54:  15000000 
INFO  @ Thu, 13 Apr 2017 18:51:55:  16000000 
INFO  @ Thu, 13 Apr 2017 18:51:57:  17000000 
INFO  @ Thu, 13 Apr 2017 18:51:58:  18000000 
INFO  @ Thu, 13 Apr 2017 18:52:00:  19000000 
INFO  @ Thu, 13 Apr 2017 18:52:01:  20000000 
INFO  @ Thu, 13 Apr 2017 18:52:03:  21000000 
INFO  @ Thu, 13 Apr 2017 18:52:04:  22000000 
INFO  @ Thu, 13 Apr 2017 18:52:06:  23000000 
INFO  @ Thu, 13 Apr 2017 18:52:08: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:52:10:  1000000 
INFO  @ Thu, 13 Apr 2017 18:52:11:  2000000 
INFO  @ Thu, 13 Apr 2017 18:52:13:  3000000 
INFO  @ Thu, 13 Apr 2017 18:52:14:  4000000 
INFO  @ Thu, 13 Apr 2017 18:52:15:  5000000 
INFO  @ Thu, 13 Apr 2017 18:52:17:  6000000 
INFO  @ Thu, 13 Apr 2017 18:52:18:  7000000 
INFO  @ Thu, 13 Apr 2017 18:52:20:  8000000 
INFO  @ Thu, 13 Apr 2017 18:52:21:  9000000 
INFO  @ Thu, 13 Apr 2017 18:52:22:  10000000 
INFO  @ Thu, 13 Apr 2017 18:52:24:  11000000 
INFO  @ Thu, 13 Apr 2017 18:52:25:  12000000 
INFO  @ Thu, 13 Apr 2017 18:52:26:  13000000 
INFO  @ Thu, 13 Apr 2017 18:52:28:  14000000 
INFO  @ Thu, 13 Apr 2017 18:52:29:  15000000 
INFO  @ Thu, 13 Apr 2017 18:52:31:  16000000 
INFO  @ Thu, 13 Apr 2017 18:52:32:  17000000 
INFO  @ Thu, 13 Apr 2017 18:52:33:  18000000 
INFO  @ Thu, 13 Apr 2017 18:52:35:  19000000 
INFO  @ Thu, 13 Apr 2017 18:52:36:  20000000 
INFO  @ Thu, 13 Apr 2017 18:52:38:  21000000 
INFO  @ Thu, 13 Apr 2017 18:52:39:  22000000 
INFO  @ Thu, 13 Apr 2017 18:52:40:  23000000 
INFO  @ Thu, 13 Apr 2017 18:52:42:  24000000 
INFO  @ Thu, 13 Apr 2017 18:52:43:  25000000 
INFO  @ Thu, 13 Apr 2017 18:52:44:  26000000 
INFO  @ Thu, 13 Apr 2017 18:52:46:  27000000 
INFO  @ Thu, 13 Apr 2017 18:52:47:  28000000 
INFO  @ Thu, 13 Apr 2017 18:52:49:  29000000 
INFO  @ Thu, 13 Apr 2017 18:52:50:  30000000 
INFO  @ Thu, 13 Apr 2017 18:52:51:  31000000 
INFO  @ Thu, 13 Apr 2017 18:52:53:  32000000 
INFO  @ Thu, 13 Apr 2017 18:52:54:  33000000 
INFO  @ Thu, 13 Apr 2017 18:52:56:  34000000 
INFO  @ Thu, 13 Apr 2017 18:52:57:  35000000 
INFO  @ Thu, 13 Apr 2017 18:52:58:  36000000 
INFO  @ Thu, 13 Apr 2017 18:53:00:  37000000 
INFO  @ Thu, 13 Apr 2017 18:53:01:  38000000 
INFO  @ Thu, 13 Apr 2017 18:53:03:  39000000 
INFO  @ Thu, 13 Apr 2017 18:53:04:  40000000 
INFO  @ Thu, 13 Apr 2017 18:53:05:  41000000 
INFO  @ Thu, 13 Apr 2017 18:53:07:  42000000 
INFO  @ Thu, 13 Apr 2017 18:53:08:  43000000 
INFO  @ Thu, 13 Apr 2017 18:53:10:  44000000 
INFO  @ Thu, 13 Apr 2017 18:53:11:  45000000 
INFO  @ Thu, 13 Apr 2017 18:53:12:  46000000 
INFO  @ Thu, 13 Apr 2017 18:53:14:  47000000 
INFO  @ Thu, 13 Apr 2017 18:53:15:  48000000 
INFO  @ Thu, 13 Apr 2017 18:53:16:  49000000 
INFO  @ Thu, 13 Apr 2017 18:53:18:  50000000 
INFO  @ Thu, 13 Apr 2017 18:53:19:  51000000 
INFO  @ Thu, 13 Apr 2017 18:53:21:  52000000 
INFO  @ Thu, 13 Apr 2017 18:53:22:  53000000 
INFO  @ Thu, 13 Apr 2017 18:53:23:  54000000 
INFO  @ Thu, 13 Apr 2017 18:53:25:  55000000 
INFO  @ Thu, 13 Apr 2017 18:53:26:  56000000 
INFO  @ Thu, 13 Apr 2017 18:53:28:  57000000 
INFO  @ Thu, 13 Apr 2017 18:53:29:  58000000 
INFO  @ Thu, 13 Apr 2017 18:53:30:  59000000 
INFO  @ Thu, 13 Apr 2017 18:53:32:  60000000 
INFO  @ Thu, 13 Apr 2017 18:53:33:  61000000 
INFO  @ Thu, 13 Apr 2017 18:53:35:  62000000 
INFO  @ Thu, 13 Apr 2017 18:53:36:  63000000 
INFO  @ Thu, 13 Apr 2017 18:53:37:  64000000 
INFO  @ Thu, 13 Apr 2017 18:53:39:  65000000 
INFO  @ Thu, 13 Apr 2017 18:53:40:  66000000 
INFO  @ Thu, 13 Apr 2017 18:53:42:  67000000 
INFO  @ Thu, 13 Apr 2017 18:53:43:  68000000 
INFO  @ Thu, 13 Apr 2017 18:53:44:  69000000 
INFO  @ Thu, 13 Apr 2017 18:53:46:  70000000 
INFO  @ Thu, 13 Apr 2017 18:53:47:  71000000 
INFO  @ Thu, 13 Apr 2017 18:53:48:  72000000 
INFO  @ Thu, 13 Apr 2017 18:53:50:  73000000 
INFO  @ Thu, 13 Apr 2017 18:53:51:  74000000 
INFO  @ Thu, 13 Apr 2017 18:53:53:  75000000 
INFO  @ Thu, 13 Apr 2017 18:53:54:  76000000 
INFO  @ Thu, 13 Apr 2017 18:53:55:  77000000 
INFO  @ Thu, 13 Apr 2017 18:53:57:  78000000 
INFO  @ Thu, 13 Apr 2017 18:53:58:  79000000 
INFO  @ Thu, 13 Apr 2017 18:54:00:  80000000 
INFO  @ Thu, 13 Apr 2017 18:54:01:  81000000 
INFO  @ Thu, 13 Apr 2017 18:54:02:  82000000 
INFO  @ Thu, 13 Apr 2017 18:54:04:  83000000 
INFO  @ Thu, 13 Apr 2017 18:54:05:  84000000 
INFO  @ Thu, 13 Apr 2017 18:54:07:  85000000 
INFO  @ Thu, 13 Apr 2017 18:54:08:  86000000 
INFO  @ Thu, 13 Apr 2017 18:54:09:  87000000 
INFO  @ Thu, 13 Apr 2017 18:54:11:  88000000 
INFO  @ Thu, 13 Apr 2017 18:54:12:  89000000 
INFO  @ Thu, 13 Apr 2017 18:54:14:  90000000 
INFO  @ Thu, 13 Apr 2017 18:54:15:  91000000 
INFO  @ Thu, 13 Apr 2017 18:54:16:  92000000 
INFO  @ Thu, 13 Apr 2017 18:54:18:  93000000 
INFO  @ Thu, 13 Apr 2017 18:54:19:  94000000 
INFO  @ Thu, 13 Apr 2017 18:54:21:  95000000 
INFO  @ Thu, 13 Apr 2017 18:54:22:  96000000 
INFO  @ Thu, 13 Apr 2017 18:54:23:  97000000 
INFO  @ Thu, 13 Apr 2017 18:54:25:  98000000 
INFO  @ Thu, 13 Apr 2017 18:54:26:  99000000 
INFO  @ Thu, 13 Apr 2017 18:54:27: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:54:27: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:54:27: #1  total tags in treatment: 23593812 
INFO  @ Thu, 13 Apr 2017 18:54:27: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:54:27: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:54:27: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:54:27: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:54:27: #2 Use 265 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:54:27: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:54:27: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:54:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 18:59:24: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:03:45: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:03:46: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:03:47: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:03:48: Done!

Num	7
ID	task.callpeak_macs2.macs2_g_b_rep2.line_155.id_16
Name	macs2 g/b rep2
Thread	thread_Root
PID	47020

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

Start	2017-04-13 18:53:18
End	2017-04-13 19:09:24
Elapsed	00:16:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 245 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz

# SYS command. line 170

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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--------------------
35307 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:53:32: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 245 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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 18:53:32: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:53:32: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:53:34:  1000000 
INFO  @ Thu, 13 Apr 2017 18:53:35:  2000000 
INFO  @ Thu, 13 Apr 2017 18:53:37:  3000000 
INFO  @ Thu, 13 Apr 2017 18:53:39:  4000000 
INFO  @ Thu, 13 Apr 2017 18:53:40:  5000000 
INFO  @ Thu, 13 Apr 2017 18:53:42:  6000000 
INFO  @ Thu, 13 Apr 2017 18:53:43:  7000000 
INFO  @ Thu, 13 Apr 2017 18:53:45:  8000000 
INFO  @ Thu, 13 Apr 2017 18:53:47:  9000000 
INFO  @ Thu, 13 Apr 2017 18:53:48:  10000000 
INFO  @ Thu, 13 Apr 2017 18:53:50:  11000000 
INFO  @ Thu, 13 Apr 2017 18:53:51:  12000000 
INFO  @ Thu, 13 Apr 2017 18:53:53:  13000000 
INFO  @ Thu, 13 Apr 2017 18:53:54:  14000000 
INFO  @ Thu, 13 Apr 2017 18:53:56:  15000000 
INFO  @ Thu, 13 Apr 2017 18:53:58:  16000000 
INFO  @ Thu, 13 Apr 2017 18:53:59:  17000000 
INFO  @ Thu, 13 Apr 2017 18:54:01:  18000000 
INFO  @ Thu, 13 Apr 2017 18:54:02:  19000000 
INFO  @ Thu, 13 Apr 2017 18:54:04:  20000000 
INFO  @ Thu, 13 Apr 2017 18:54:05:  21000000 
INFO  @ Thu, 13 Apr 2017 18:54:07:  22000000 
INFO  @ Thu, 13 Apr 2017 18:54:09:  23000000 
INFO  @ Thu, 13 Apr 2017 18:54:10:  24000000 
INFO  @ Thu, 13 Apr 2017 18:54:12:  25000000 
INFO  @ Thu, 13 Apr 2017 18:54:13:  26000000 
INFO  @ Thu, 13 Apr 2017 18:54:15:  27000000 
INFO  @ Thu, 13 Apr 2017 18:54:17:  28000000 
INFO  @ Thu, 13 Apr 2017 18:54:18:  29000000 
INFO  @ Thu, 13 Apr 2017 18:54:20:  30000000 
INFO  @ Thu, 13 Apr 2017 18:54:21:  31000000 
INFO  @ Thu, 13 Apr 2017 18:54:23:  32000000 
INFO  @ Thu, 13 Apr 2017 18:54:24:  33000000 
INFO  @ Thu, 13 Apr 2017 18:54:26:  34000000 
INFO  @ Thu, 13 Apr 2017 18:54:28:  35000000 
INFO  @ Thu, 13 Apr 2017 18:54:29:  36000000 
INFO  @ Thu, 13 Apr 2017 18:54:31:  37000000 
INFO  @ Thu, 13 Apr 2017 18:54:32:  38000000 
INFO  @ Thu, 13 Apr 2017 18:54:34:  39000000 
INFO  @ Thu, 13 Apr 2017 18:54:35:  40000000 
INFO  @ Thu, 13 Apr 2017 18:54:37:  41000000 
INFO  @ Thu, 13 Apr 2017 18:54:38:  42000000 
INFO  @ Thu, 13 Apr 2017 18:54:40:  43000000 
INFO  @ Thu, 13 Apr 2017 18:54:42:  44000000 
INFO  @ Thu, 13 Apr 2017 18:54:43:  45000000 
INFO  @ Thu, 13 Apr 2017 18:54:45:  46000000 
INFO  @ Thu, 13 Apr 2017 18:54:47:  47000000 
INFO  @ Thu, 13 Apr 2017 18:54:48:  48000000 
INFO  @ Thu, 13 Apr 2017 18:54:50:  49000000 
INFO  @ Thu, 13 Apr 2017 18:54:51:  50000000 
INFO  @ Thu, 13 Apr 2017 18:54:53:  51000000 
INFO  @ Thu, 13 Apr 2017 18:54:55:  52000000 
INFO  @ Thu, 13 Apr 2017 18:54:56:  53000000 
INFO  @ Thu, 13 Apr 2017 18:54:58:  54000000 
INFO  @ Thu, 13 Apr 2017 18:54:59:  55000000 
INFO  @ Thu, 13 Apr 2017 18:55:01:  56000000 
INFO  @ Thu, 13 Apr 2017 18:55:03:  57000000 
INFO  @ Thu, 13 Apr 2017 18:55:05:  58000000 
INFO  @ Thu, 13 Apr 2017 18:55:06:  59000000 
INFO  @ Thu, 13 Apr 2017 18:55:08:  60000000 
INFO  @ Thu, 13 Apr 2017 18:55:09:  61000000 
INFO  @ Thu, 13 Apr 2017 18:55:11:  62000000 
INFO  @ Thu, 13 Apr 2017 18:55:12:  63000000 
INFO  @ Thu, 13 Apr 2017 18:55:14:  64000000 
INFO  @ Thu, 13 Apr 2017 18:55:16:  65000000 
INFO  @ Thu, 13 Apr 2017 18:55:17:  66000000 
INFO  @ Thu, 13 Apr 2017 18:55:19:  67000000 
INFO  @ Thu, 13 Apr 2017 18:55:20:  68000000 
INFO  @ Thu, 13 Apr 2017 18:55:26: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:55:28:  1000000 
INFO  @ Thu, 13 Apr 2017 18:55:29:  2000000 
INFO  @ Thu, 13 Apr 2017 18:55:30:  3000000 
INFO  @ Thu, 13 Apr 2017 18:55:32:  4000000 
INFO  @ Thu, 13 Apr 2017 18:55:33:  5000000 
INFO  @ Thu, 13 Apr 2017 18:55:35:  6000000 
INFO  @ Thu, 13 Apr 2017 18:55:36:  7000000 
INFO  @ Thu, 13 Apr 2017 18:55:38:  8000000 
INFO  @ Thu, 13 Apr 2017 18:55:39:  9000000 
INFO  @ Thu, 13 Apr 2017 18:55:41:  10000000 
INFO  @ Thu, 13 Apr 2017 18:55:42:  11000000 
INFO  @ Thu, 13 Apr 2017 18:55:44:  12000000 
INFO  @ Thu, 13 Apr 2017 18:55:45:  13000000 
INFO  @ Thu, 13 Apr 2017 18:55:46:  14000000 
INFO  @ Thu, 13 Apr 2017 18:55:48:  15000000 
INFO  @ Thu, 13 Apr 2017 18:55:49:  16000000 
INFO  @ Thu, 13 Apr 2017 18:55:51:  17000000 
INFO  @ Thu, 13 Apr 2017 18:55:52:  18000000 
INFO  @ Thu, 13 Apr 2017 18:55:54:  19000000 
INFO  @ Thu, 13 Apr 2017 18:55:55:  20000000 
INFO  @ Thu, 13 Apr 2017 18:55:57:  21000000 
INFO  @ Thu, 13 Apr 2017 18:55:58:  22000000 
INFO  @ Thu, 13 Apr 2017 18:56:00:  23000000 
INFO  @ Thu, 13 Apr 2017 18:56:01:  24000000 
INFO  @ Thu, 13 Apr 2017 18:56:02:  25000000 
INFO  @ Thu, 13 Apr 2017 18:56:04:  26000000 
INFO  @ Thu, 13 Apr 2017 18:56:05:  27000000 
INFO  @ Thu, 13 Apr 2017 18:56:07:  28000000 
INFO  @ Thu, 13 Apr 2017 18:56:08:  29000000 
INFO  @ Thu, 13 Apr 2017 18:56:10:  30000000 
INFO  @ Thu, 13 Apr 2017 18:56:11:  31000000 
INFO  @ Thu, 13 Apr 2017 18:56:13:  32000000 
INFO  @ Thu, 13 Apr 2017 18:56:14:  33000000 
INFO  @ Thu, 13 Apr 2017 18:56:15:  34000000 
INFO  @ Thu, 13 Apr 2017 18:56:17:  35000000 
INFO  @ Thu, 13 Apr 2017 18:56:18:  36000000 
INFO  @ Thu, 13 Apr 2017 18:56:20:  37000000 
INFO  @ Thu, 13 Apr 2017 18:56:21:  38000000 
INFO  @ Thu, 13 Apr 2017 18:56:23:  39000000 
INFO  @ Thu, 13 Apr 2017 18:56:24:  40000000 
INFO  @ Thu, 13 Apr 2017 18:56:25:  41000000 
INFO  @ Thu, 13 Apr 2017 18:56:27:  42000000 
INFO  @ Thu, 13 Apr 2017 18:56:28:  43000000 
INFO  @ Thu, 13 Apr 2017 18:56:30:  44000000 
INFO  @ Thu, 13 Apr 2017 18:56:31:  45000000 
INFO  @ Thu, 13 Apr 2017 18:56:33:  46000000 
INFO  @ Thu, 13 Apr 2017 18:56:34:  47000000 
INFO  @ Thu, 13 Apr 2017 18:56:36:  48000000 
INFO  @ Thu, 13 Apr 2017 18:56:37:  49000000 
INFO  @ Thu, 13 Apr 2017 18:56:39:  50000000 
INFO  @ Thu, 13 Apr 2017 18:56:41:  51000000 
INFO  @ Thu, 13 Apr 2017 18:56:42:  52000000 
INFO  @ Thu, 13 Apr 2017 18:56:43:  53000000 
INFO  @ Thu, 13 Apr 2017 18:56:45:  54000000 
INFO  @ Thu, 13 Apr 2017 18:56:46:  55000000 
INFO  @ Thu, 13 Apr 2017 18:56:48:  56000000 
INFO  @ Thu, 13 Apr 2017 18:56:49:  57000000 
INFO  @ Thu, 13 Apr 2017 18:56:51:  58000000 
INFO  @ Thu, 13 Apr 2017 18:56:52:  59000000 
INFO  @ Thu, 13 Apr 2017 18:56:54:  60000000 
INFO  @ Thu, 13 Apr 2017 18:56:55:  61000000 
INFO  @ Thu, 13 Apr 2017 18:56:57:  62000000 
INFO  @ Thu, 13 Apr 2017 18:56:58:  63000000 
INFO  @ Thu, 13 Apr 2017 18:57:00:  64000000 
INFO  @ Thu, 13 Apr 2017 18:57:01:  65000000 
INFO  @ Thu, 13 Apr 2017 18:57:03:  66000000 
INFO  @ Thu, 13 Apr 2017 18:57:04:  67000000 
INFO  @ Thu, 13 Apr 2017 18:57:05:  68000000 
INFO  @ Thu, 13 Apr 2017 18:57:07:  69000000 
INFO  @ Thu, 13 Apr 2017 18:57:08:  70000000 
INFO  @ Thu, 13 Apr 2017 18:57:10:  71000000 
INFO  @ Thu, 13 Apr 2017 18:57:11:  72000000 
INFO  @ Thu, 13 Apr 2017 18:57:13:  73000000 
INFO  @ Thu, 13 Apr 2017 18:57:14:  74000000 
INFO  @ Thu, 13 Apr 2017 18:57:16:  75000000 
INFO  @ Thu, 13 Apr 2017 18:57:17:  76000000 
INFO  @ Thu, 13 Apr 2017 18:57:19:  77000000 
INFO  @ Thu, 13 Apr 2017 18:57:20:  78000000 
INFO  @ Thu, 13 Apr 2017 18:57:22:  79000000 
INFO  @ Thu, 13 Apr 2017 18:57:23:  80000000 
INFO  @ Thu, 13 Apr 2017 18:57:24:  81000000 
INFO  @ Thu, 13 Apr 2017 18:57:26:  82000000 
INFO  @ Thu, 13 Apr 2017 18:57:27:  83000000 
INFO  @ Thu, 13 Apr 2017 18:57:29:  84000000 
INFO  @ Thu, 13 Apr 2017 18:57:30:  85000000 
INFO  @ Thu, 13 Apr 2017 18:57:32:  86000000 
INFO  @ Thu, 13 Apr 2017 18:57:33:  87000000 
INFO  @ Thu, 13 Apr 2017 18:57:35:  88000000 
INFO  @ Thu, 13 Apr 2017 18:57:36:  89000000 
INFO  @ Thu, 13 Apr 2017 18:57:38:  90000000 
INFO  @ Thu, 13 Apr 2017 18:57:39:  91000000 
INFO  @ Thu, 13 Apr 2017 18:57:41:  92000000 
INFO  @ Thu, 13 Apr 2017 18:57:42:  93000000 
INFO  @ Thu, 13 Apr 2017 18:57:44:  94000000 
INFO  @ Thu, 13 Apr 2017 18:57:45:  95000000 
INFO  @ Thu, 13 Apr 2017 18:57:46:  96000000 
INFO  @ Thu, 13 Apr 2017 18:57:48:  97000000 
INFO  @ Thu, 13 Apr 2017 18:57:49:  98000000 
INFO  @ Thu, 13 Apr 2017 18:57:51:  99000000 
INFO  @ Thu, 13 Apr 2017 18:57:52: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:57:52: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:57:52: #1  total tags in treatment: 68407958 
INFO  @ Thu, 13 Apr 2017 18:57:52: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:57:52: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:57:52: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:57:52: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:57:52: #2 Use 245 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:57:52: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:57:52: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:57:52: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:03:55: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:09:15: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:09:17: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:09:19: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:09:20: 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	47021

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

Start	2017-04-13 18:53:38
End	2017-04-13 19:07:02
Elapsed	00:13:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 245 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.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--------------------
30375 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:54:02: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 245 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF078YAS.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 18:54:02: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:54:02: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:54:03:  1000000 
INFO  @ Thu, 13 Apr 2017 18:54:05:  2000000 
INFO  @ Thu, 13 Apr 2017 18:54:07:  3000000 
INFO  @ Thu, 13 Apr 2017 18:54:08:  4000000 
INFO  @ Thu, 13 Apr 2017 18:54:10:  5000000 
INFO  @ Thu, 13 Apr 2017 18:54:12:  6000000 
INFO  @ Thu, 13 Apr 2017 18:54:13:  7000000 
INFO  @ Thu, 13 Apr 2017 18:54:15:  8000000 
INFO  @ Thu, 13 Apr 2017 18:54:16:  9000000 
INFO  @ Thu, 13 Apr 2017 18:54:18:  10000000 
INFO  @ Thu, 13 Apr 2017 18:54:20:  11000000 
INFO  @ Thu, 13 Apr 2017 18:54:21:  12000000 
INFO  @ Thu, 13 Apr 2017 18:54:23:  13000000 
INFO  @ Thu, 13 Apr 2017 18:54:24:  14000000 
INFO  @ Thu, 13 Apr 2017 18:54:26:  15000000 
INFO  @ Thu, 13 Apr 2017 18:54:28:  16000000 
INFO  @ Thu, 13 Apr 2017 18:54:29:  17000000 
INFO  @ Thu, 13 Apr 2017 18:54:31:  18000000 
INFO  @ Thu, 13 Apr 2017 18:54:33:  19000000 
INFO  @ Thu, 13 Apr 2017 18:54:34:  20000000 
INFO  @ Thu, 13 Apr 2017 18:54:36:  21000000 
INFO  @ Thu, 13 Apr 2017 18:54:37:  22000000 
INFO  @ Thu, 13 Apr 2017 18:54:39:  23000000 
INFO  @ Thu, 13 Apr 2017 18:54:41:  24000000 
INFO  @ Thu, 13 Apr 2017 18:54:42:  25000000 
INFO  @ Thu, 13 Apr 2017 18:54:44:  26000000 
INFO  @ Thu, 13 Apr 2017 18:54:46:  27000000 
INFO  @ Thu, 13 Apr 2017 18:54:47:  28000000 
INFO  @ Thu, 13 Apr 2017 18:54:49:  29000000 
INFO  @ Thu, 13 Apr 2017 18:54:51:  30000000 
INFO  @ Thu, 13 Apr 2017 18:54:52:  31000000 
INFO  @ Thu, 13 Apr 2017 18:54:54:  32000000 
INFO  @ Thu, 13 Apr 2017 18:54:55:  33000000 
INFO  @ Thu, 13 Apr 2017 18:54:57:  34000000 
INFO  @ Thu, 13 Apr 2017 18:55:00: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:55:01:  1000000 
INFO  @ Thu, 13 Apr 2017 18:55:03:  2000000 
INFO  @ Thu, 13 Apr 2017 18:55:04:  3000000 
INFO  @ Thu, 13 Apr 2017 18:55:06:  4000000 
INFO  @ Thu, 13 Apr 2017 18:55:07:  5000000 
INFO  @ Thu, 13 Apr 2017 18:55:09:  6000000 
INFO  @ Thu, 13 Apr 2017 18:55:10:  7000000 
INFO  @ Thu, 13 Apr 2017 18:55:11:  8000000 
INFO  @ Thu, 13 Apr 2017 18:55:13:  9000000 
INFO  @ Thu, 13 Apr 2017 18:55:14:  10000000 
INFO  @ Thu, 13 Apr 2017 18:55:16:  11000000 
INFO  @ Thu, 13 Apr 2017 18:55:17:  12000000 
INFO  @ Thu, 13 Apr 2017 18:55:18:  13000000 
INFO  @ Thu, 13 Apr 2017 18:55:20:  14000000 
INFO  @ Thu, 13 Apr 2017 18:55:21:  15000000 
INFO  @ Thu, 13 Apr 2017 18:55:23:  16000000 
INFO  @ Thu, 13 Apr 2017 18:55:24:  17000000 
INFO  @ Thu, 13 Apr 2017 18:55:25:  18000000 
INFO  @ Thu, 13 Apr 2017 18:55:27:  19000000 
INFO  @ Thu, 13 Apr 2017 18:55:28:  20000000 
INFO  @ Thu, 13 Apr 2017 18:55:30:  21000000 
INFO  @ Thu, 13 Apr 2017 18:55:31:  22000000 
INFO  @ Thu, 13 Apr 2017 18:55:33:  23000000 
INFO  @ Thu, 13 Apr 2017 18:55:34:  24000000 
INFO  @ Thu, 13 Apr 2017 18:55:35:  25000000 
INFO  @ Thu, 13 Apr 2017 18:55:37:  26000000 
INFO  @ Thu, 13 Apr 2017 18:55:38:  27000000 
INFO  @ Thu, 13 Apr 2017 18:55:40:  28000000 
INFO  @ Thu, 13 Apr 2017 18:55:41:  29000000 
INFO  @ Thu, 13 Apr 2017 18:55:43:  30000000 
INFO  @ Thu, 13 Apr 2017 18:55:44:  31000000 
INFO  @ Thu, 13 Apr 2017 18:55:45:  32000000 
INFO  @ Thu, 13 Apr 2017 18:55:47:  33000000 
INFO  @ Thu, 13 Apr 2017 18:55:48:  34000000 
INFO  @ Thu, 13 Apr 2017 18:55:50:  35000000 
INFO  @ Thu, 13 Apr 2017 18:55:51:  36000000 
INFO  @ Thu, 13 Apr 2017 18:55:52:  37000000 
INFO  @ Thu, 13 Apr 2017 18:55:54:  38000000 
INFO  @ Thu, 13 Apr 2017 18:55:55:  39000000 
INFO  @ Thu, 13 Apr 2017 18:55:56:  40000000 
INFO  @ Thu, 13 Apr 2017 18:55:58:  41000000 
INFO  @ Thu, 13 Apr 2017 18:55:59:  42000000 
INFO  @ Thu, 13 Apr 2017 18:56:01:  43000000 
INFO  @ Thu, 13 Apr 2017 18:56:02:  44000000 
INFO  @ Thu, 13 Apr 2017 18:56:03:  45000000 
INFO  @ Thu, 13 Apr 2017 18:56:05:  46000000 
INFO  @ Thu, 13 Apr 2017 18:56:06:  47000000 
INFO  @ Thu, 13 Apr 2017 18:56:08:  48000000 
INFO  @ Thu, 13 Apr 2017 18:56:09:  49000000 
INFO  @ Thu, 13 Apr 2017 18:56:10:  50000000 
INFO  @ Thu, 13 Apr 2017 18:56:12:  51000000 
INFO  @ Thu, 13 Apr 2017 18:56:13:  52000000 
INFO  @ Thu, 13 Apr 2017 18:56:15:  53000000 
INFO  @ Thu, 13 Apr 2017 18:56:16:  54000000 
INFO  @ Thu, 13 Apr 2017 18:56:17:  55000000 
INFO  @ Thu, 13 Apr 2017 18:56:19:  56000000 
INFO  @ Thu, 13 Apr 2017 18:56:20:  57000000 
INFO  @ Thu, 13 Apr 2017 18:56:21:  58000000 
INFO  @ Thu, 13 Apr 2017 18:56:23:  59000000 
INFO  @ Thu, 13 Apr 2017 18:56:24:  60000000 
INFO  @ Thu, 13 Apr 2017 18:56:26:  61000000 
INFO  @ Thu, 13 Apr 2017 18:56:27:  62000000 
INFO  @ Thu, 13 Apr 2017 18:56:28:  63000000 
INFO  @ Thu, 13 Apr 2017 18:56:30:  64000000 
INFO  @ Thu, 13 Apr 2017 18:56:31:  65000000 
INFO  @ Thu, 13 Apr 2017 18:56:33:  66000000 
INFO  @ Thu, 13 Apr 2017 18:56:34:  67000000 
INFO  @ Thu, 13 Apr 2017 18:56:35:  68000000 
INFO  @ Thu, 13 Apr 2017 18:56:37:  69000000 
INFO  @ Thu, 13 Apr 2017 18:56:38:  70000000 
INFO  @ Thu, 13 Apr 2017 18:56:40:  71000000 
INFO  @ Thu, 13 Apr 2017 18:56:41:  72000000 
INFO  @ Thu, 13 Apr 2017 18:56:42:  73000000 
INFO  @ Thu, 13 Apr 2017 18:56:44:  74000000 
INFO  @ Thu, 13 Apr 2017 18:56:45:  75000000 
INFO  @ Thu, 13 Apr 2017 18:56:46:  76000000 
INFO  @ Thu, 13 Apr 2017 18:56:48:  77000000 
INFO  @ Thu, 13 Apr 2017 18:56:49:  78000000 
INFO  @ Thu, 13 Apr 2017 18:56:51:  79000000 
INFO  @ Thu, 13 Apr 2017 18:56:52:  80000000 
INFO  @ Thu, 13 Apr 2017 18:56:53:  81000000 
INFO  @ Thu, 13 Apr 2017 18:56:55:  82000000 
INFO  @ Thu, 13 Apr 2017 18:56:56:  83000000 
INFO  @ Thu, 13 Apr 2017 18:56:58:  84000000 
INFO  @ Thu, 13 Apr 2017 18:56:59:  85000000 
INFO  @ Thu, 13 Apr 2017 18:57:00:  86000000 
INFO  @ Thu, 13 Apr 2017 18:57:02:  87000000 
INFO  @ Thu, 13 Apr 2017 18:57:03:  88000000 
INFO  @ Thu, 13 Apr 2017 18:57:05:  89000000 
INFO  @ Thu, 13 Apr 2017 18:57:06:  90000000 
INFO  @ Thu, 13 Apr 2017 18:57:07:  91000000 
INFO  @ Thu, 13 Apr 2017 18:57:09:  92000000 
INFO  @ Thu, 13 Apr 2017 18:57:10:  93000000 
INFO  @ Thu, 13 Apr 2017 18:57:12:  94000000 
INFO  @ Thu, 13 Apr 2017 18:57:13:  95000000 
INFO  @ Thu, 13 Apr 2017 18:57:14:  96000000 
INFO  @ Thu, 13 Apr 2017 18:57:16:  97000000 
INFO  @ Thu, 13 Apr 2017 18:57:17:  98000000 
INFO  @ Thu, 13 Apr 2017 18:57:18:  99000000 
INFO  @ Thu, 13 Apr 2017 18:57:20: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 18:57:20: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 18:57:20: #1  total tags in treatment: 34203980 
INFO  @ Thu, 13 Apr 2017 18:57:20: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 18:57:20: #1 finished! 
INFO  @ Thu, 13 Apr 2017 18:57:20: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 18:57:20: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 18:57:20: #2 Use 245 as fragment length 
INFO  @ Thu, 13 Apr 2017 18:57:20: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 18:57:20: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 18:57:20: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:02:21: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:06:53: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:06:55: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:06:56: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:06:57: 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	47028

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

Start	2017-04-13 18:57:57
End	2017-04-13 19:18:06
Elapsed	00:20:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 245 --keep-dup all

# SYS command. line 166

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.broadPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.gappedPeak \
		  "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.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--------------------
21548 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
INFO  @ Thu, 13 Apr 2017 18:58:17: 
# Command line: callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --broad --nomodel --shift 0 --extsize 245 --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign
# format = BED
# ChIP-seq file = ['/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF078YAS.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 18:58:17: #1 read tag files... 
INFO  @ Thu, 13 Apr 2017 18:58:17: #1 read treatment tags... 
INFO  @ Thu, 13 Apr 2017 18:58:19:  1000000 
INFO  @ Thu, 13 Apr 2017 18:58:21:  2000000 
INFO  @ Thu, 13 Apr 2017 18:58:24:  3000000 
INFO  @ Thu, 13 Apr 2017 18:58:26:  4000000 
INFO  @ Thu, 13 Apr 2017 18:58:28:  5000000 
INFO  @ Thu, 13 Apr 2017 18:58:30:  6000000 
INFO  @ Thu, 13 Apr 2017 18:58:32:  7000000 
INFO  @ Thu, 13 Apr 2017 18:58:35:  8000000 
INFO  @ Thu, 13 Apr 2017 18:58:37:  9000000 
INFO  @ Thu, 13 Apr 2017 18:58:39:  10000000 
INFO  @ Thu, 13 Apr 2017 18:58:41:  11000000 
INFO  @ Thu, 13 Apr 2017 18:58:44:  12000000 
INFO  @ Thu, 13 Apr 2017 18:58:46:  13000000 
INFO  @ Thu, 13 Apr 2017 18:58:48:  14000000 
INFO  @ Thu, 13 Apr 2017 18:58:50:  15000000 
INFO  @ Thu, 13 Apr 2017 18:58:53:  16000000 
INFO  @ Thu, 13 Apr 2017 18:58:55:  17000000 
INFO  @ Thu, 13 Apr 2017 18:58:57:  18000000 
INFO  @ Thu, 13 Apr 2017 18:58:59:  19000000 
INFO  @ Thu, 13 Apr 2017 18:59:02:  20000000 
INFO  @ Thu, 13 Apr 2017 18:59:04:  21000000 
INFO  @ Thu, 13 Apr 2017 18:59:06:  22000000 
INFO  @ Thu, 13 Apr 2017 18:59:08:  23000000 
INFO  @ Thu, 13 Apr 2017 18:59:10:  24000000 
INFO  @ Thu, 13 Apr 2017 18:59:12:  25000000 
INFO  @ Thu, 13 Apr 2017 18:59:15:  26000000 
INFO  @ Thu, 13 Apr 2017 18:59:17:  27000000 
INFO  @ Thu, 13 Apr 2017 18:59:19:  28000000 
INFO  @ Thu, 13 Apr 2017 18:59:21:  29000000 
INFO  @ Thu, 13 Apr 2017 18:59:23:  30000000 
INFO  @ Thu, 13 Apr 2017 18:59:25:  31000000 
INFO  @ Thu, 13 Apr 2017 18:59:28:  32000000 
INFO  @ Thu, 13 Apr 2017 18:59:30:  33000000 
INFO  @ Thu, 13 Apr 2017 18:59:32:  34000000 
INFO  @ Thu, 13 Apr 2017 18:59:35: #1.2 read input tags... 
INFO  @ Thu, 13 Apr 2017 18:59:38:  1000000 
INFO  @ Thu, 13 Apr 2017 18:59:39:  2000000 
INFO  @ Thu, 13 Apr 2017 18:59:42:  3000000 
INFO  @ Thu, 13 Apr 2017 18:59:43:  4000000 
INFO  @ Thu, 13 Apr 2017 18:59:46:  5000000 
INFO  @ Thu, 13 Apr 2017 18:59:48:  6000000 
INFO  @ Thu, 13 Apr 2017 18:59:50:  7000000 
INFO  @ Thu, 13 Apr 2017 18:59:52:  8000000 
INFO  @ Thu, 13 Apr 2017 18:59:54:  9000000 
INFO  @ Thu, 13 Apr 2017 18:59:56:  10000000 
INFO  @ Thu, 13 Apr 2017 18:59:58:  11000000 
INFO  @ Thu, 13 Apr 2017 19:00:00:  12000000 
INFO  @ Thu, 13 Apr 2017 19:00:02:  13000000 
INFO  @ Thu, 13 Apr 2017 19:00:04:  14000000 
INFO  @ Thu, 13 Apr 2017 19:00:06:  15000000 
INFO  @ Thu, 13 Apr 2017 19:00:08:  16000000 
INFO  @ Thu, 13 Apr 2017 19:00:10:  17000000 
INFO  @ Thu, 13 Apr 2017 19:00:12:  18000000 
INFO  @ Thu, 13 Apr 2017 19:00:14:  19000000 
INFO  @ Thu, 13 Apr 2017 19:00:16:  20000000 
INFO  @ Thu, 13 Apr 2017 19:00:18:  21000000 
INFO  @ Thu, 13 Apr 2017 19:00:20:  22000000 
INFO  @ Thu, 13 Apr 2017 19:00:23:  23000000 
INFO  @ Thu, 13 Apr 2017 19:00:25:  24000000 
INFO  @ Thu, 13 Apr 2017 19:00:27:  25000000 
INFO  @ Thu, 13 Apr 2017 19:00:29:  26000000 
INFO  @ Thu, 13 Apr 2017 19:00:31:  27000000 
INFO  @ Thu, 13 Apr 2017 19:00:33:  28000000 
INFO  @ Thu, 13 Apr 2017 19:00:35:  29000000 
INFO  @ Thu, 13 Apr 2017 19:00:37:  30000000 
INFO  @ Thu, 13 Apr 2017 19:00:39:  31000000 
INFO  @ Thu, 13 Apr 2017 19:00:41:  32000000 
INFO  @ Thu, 13 Apr 2017 19:00:43:  33000000 
INFO  @ Thu, 13 Apr 2017 19:00:45:  34000000 
INFO  @ Thu, 13 Apr 2017 19:00:47:  35000000 
INFO  @ Thu, 13 Apr 2017 19:00:49:  36000000 
INFO  @ Thu, 13 Apr 2017 19:00:51:  37000000 
INFO  @ Thu, 13 Apr 2017 19:00:53:  38000000 
INFO  @ Thu, 13 Apr 2017 19:00:55:  39000000 
INFO  @ Thu, 13 Apr 2017 19:00:57:  40000000 
INFO  @ Thu, 13 Apr 2017 19:00:59:  41000000 
INFO  @ Thu, 13 Apr 2017 19:01:01:  42000000 
INFO  @ Thu, 13 Apr 2017 19:01:03:  43000000 
INFO  @ Thu, 13 Apr 2017 19:01:05:  44000000 
INFO  @ Thu, 13 Apr 2017 19:01:07:  45000000 
INFO  @ Thu, 13 Apr 2017 19:01:10:  46000000 
INFO  @ Thu, 13 Apr 2017 19:01:12:  47000000 
INFO  @ Thu, 13 Apr 2017 19:01:14:  48000000 
INFO  @ Thu, 13 Apr 2017 19:01:16:  49000000 
INFO  @ Thu, 13 Apr 2017 19:01:18:  50000000 
INFO  @ Thu, 13 Apr 2017 19:01:20:  51000000 
INFO  @ Thu, 13 Apr 2017 19:01:22:  52000000 
INFO  @ Thu, 13 Apr 2017 19:01:24:  53000000 
INFO  @ Thu, 13 Apr 2017 19:01:26:  54000000 
INFO  @ Thu, 13 Apr 2017 19:01:28:  55000000 
INFO  @ Thu, 13 Apr 2017 19:01:30:  56000000 
INFO  @ Thu, 13 Apr 2017 19:01:32:  57000000 
INFO  @ Thu, 13 Apr 2017 19:01:34:  58000000 
INFO  @ Thu, 13 Apr 2017 19:01:36:  59000000 
INFO  @ Thu, 13 Apr 2017 19:01:39:  60000000 
INFO  @ Thu, 13 Apr 2017 19:01:41:  61000000 
INFO  @ Thu, 13 Apr 2017 19:01:43:  62000000 
INFO  @ Thu, 13 Apr 2017 19:01:45:  63000000 
INFO  @ Thu, 13 Apr 2017 19:01:47:  64000000 
INFO  @ Thu, 13 Apr 2017 19:01:49:  65000000 
INFO  @ Thu, 13 Apr 2017 19:01:51:  66000000 
INFO  @ Thu, 13 Apr 2017 19:01:53:  67000000 
INFO  @ Thu, 13 Apr 2017 19:01:55:  68000000 
INFO  @ Thu, 13 Apr 2017 19:01:58:  69000000 
INFO  @ Thu, 13 Apr 2017 19:02:00:  70000000 
INFO  @ Thu, 13 Apr 2017 19:02:02:  71000000 
INFO  @ Thu, 13 Apr 2017 19:02:04:  72000000 
INFO  @ Thu, 13 Apr 2017 19:02:06:  73000000 
INFO  @ Thu, 13 Apr 2017 19:02:08:  74000000 
INFO  @ Thu, 13 Apr 2017 19:02:10:  75000000 
INFO  @ Thu, 13 Apr 2017 19:02:12:  76000000 
INFO  @ Thu, 13 Apr 2017 19:02:14:  77000000 
INFO  @ Thu, 13 Apr 2017 19:02:16:  78000000 
INFO  @ Thu, 13 Apr 2017 19:02:19:  79000000 
INFO  @ Thu, 13 Apr 2017 19:02:21:  80000000 
INFO  @ Thu, 13 Apr 2017 19:02:23:  81000000 
INFO  @ Thu, 13 Apr 2017 19:02:25:  82000000 
INFO  @ Thu, 13 Apr 2017 19:02:27:  83000000 
INFO  @ Thu, 13 Apr 2017 19:02:29:  84000000 
INFO  @ Thu, 13 Apr 2017 19:02:31:  85000000 
INFO  @ Thu, 13 Apr 2017 19:02:33:  86000000 
INFO  @ Thu, 13 Apr 2017 19:02:35:  87000000 
INFO  @ Thu, 13 Apr 2017 19:02:37:  88000000 
INFO  @ Thu, 13 Apr 2017 19:02:39:  89000000 
INFO  @ Thu, 13 Apr 2017 19:02:41:  90000000 
INFO  @ Thu, 13 Apr 2017 19:02:44:  91000000 
INFO  @ Thu, 13 Apr 2017 19:02:46:  92000000 
INFO  @ Thu, 13 Apr 2017 19:02:48:  93000000 
INFO  @ Thu, 13 Apr 2017 19:02:50:  94000000 
INFO  @ Thu, 13 Apr 2017 19:02:52:  95000000 
INFO  @ Thu, 13 Apr 2017 19:02:54:  96000000 
INFO  @ Thu, 13 Apr 2017 19:02:56:  97000000 
INFO  @ Thu, 13 Apr 2017 19:02:58:  98000000 
INFO  @ Thu, 13 Apr 2017 19:03:00:  99000000 
INFO  @ Thu, 13 Apr 2017 19:03:02: #1 tag size is determined as 101 bps 
INFO  @ Thu, 13 Apr 2017 19:03:02: #1 tag size = 101 
INFO  @ Thu, 13 Apr 2017 19:03:02: #1  total tags in treatment: 34203978 
INFO  @ Thu, 13 Apr 2017 19:03:02: #1  total tags in control: 99493262 
INFO  @ Thu, 13 Apr 2017 19:03:02: #1 finished! 
INFO  @ Thu, 13 Apr 2017 19:03:02: #2 Build Peak Model... 
INFO  @ Thu, 13 Apr 2017 19:03:02: #2 Skipped... 
INFO  @ Thu, 13 Apr 2017 19:03:02: #2 Use 245 as fragment length 
INFO  @ Thu, 13 Apr 2017 19:03:02: #3 Call peaks... 
INFO  @ Thu, 13 Apr 2017 19:03:02: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Thu, 13 Apr 2017 19:03:02: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Thu, 13 Apr 2017 19:11:52: #3 Call peaks for each chromosome... 
INFO  @ Thu, 13 Apr 2017 19:17:54: #4 Write output xls file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.xls 
INFO  @ Thu, 13 Apr 2017 19:17:56: #4 Write broad peak in broadPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.broadPeak 
INFO  @ Thu, 13 Apr 2017 19:17:58: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign_peaks.gappedPeak 
INFO  @ Thu, 13 Apr 2017 19:17:59: Done!

Num	10
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_19
Name	naive_overlap
Thread	thread_Root
PID	47035

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

Start	2017-04-13 19:18:09
End	2017-04-13 19:19:30
Elapsed	00:01:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.gappedPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.gappedPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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--------------------
35935 (process ID) old priority 0, new priority 19
Waiting for 53 seconds.

Num	11
ID	task.callpeak_naive_overlap.naive_overlap.line_143.id_20
Name	naive_overlap
Thread	thread_Root
PID	47036

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

Start	2017-04-13 19:18:10
End	2017-04-13 19:19:30
Elapsed	00:01:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/rep1/ENCFF057NJA.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/ZBTB17_MACS2/out/peak/macs2/rep2/ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz) -b <(zcat -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz

# SYS command. line 154

 zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInPsRep1AndPsRep2.broadPeak.gz | sort | uniq | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.PooledInReps.broadPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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--------------------
35936 (process ID) old priority 0, new priority 19
Waiting for 55 seconds.

Num	12
ID	task.report.peak2hammock.line_361.id_23
Name	peak2hammock
Thread	thread_Root
PID	39017

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

Start	2017-04-13 19:19:35
End	2017-04-13 19:19:46
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Output files	/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.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/ZBTB17_MACS2/out/peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.tmp

   
--------------------Stdout--------------------
39021 (process ID) old priority 0, new priority 19

Num	13
ID	task.graphviz.report.line_97.id_24
Name	report
Thread	thread_Root
PID	39558

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

Start	2017-04-13 19:19:48
End	2017-04-13 19:19:56
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/ZBTB17_MACS2/out/report/ZBTB17_MACS2_workflow.dot > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/report/ZBTB17_MACS2_workflow.svg 2> /dev/null || echo "svg: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/report/ZBTB17_MACS2_workflow.svg" # to suppress dot font error (exit code=1)

   
--------------------Stdout--------------------
39562 (process ID) old priority 0, new priority 19

Type	Name	Value
string	_	/usr/bin/bds
bool	allowEmpty	false
string[]	args	[-title, ZBTB17_MACS2, -nth, 5, -species, hg38_ENCODE, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.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/ZBTB17_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/ZBTB17_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	45973.ZBTB17_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

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope