BigDataScript report: chipseq.bds

Script file /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20170413_124933_982
Start time 2017-04-13 12:49:33
Run time 00:00:56.881
Tasks executed 9
Tasks failed 9
Tasks failed names 
macs2 n/s ppr1
macs2 n/s rep2-pr1
macs2 n/s pooled_rep
macs2 n/s rep1-pr2
macs2 n/s rep1-pr1
macs2 n/s rep2-pr2
macs2 n/s ppr2
macs2 n/s rep2
macs2 n/s rep1
Arguments* [-title, ZIC2_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]
System* sge
Cpus* -1
Exit value 1
* Values in global scope when program finished execution.

Timeline

Task Graph

Parallel (threads) details

Thread ID Parent Tasks
thread_Root None 
 chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17
chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18
thread_41 thread_Root
thread_42 thread_Root
thread_43 thread_Root

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10
Name macs2 n/s pooled_rep
Thread thread_Root
PID 46780
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:49:46
End 2017-04-13 12:49:46
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep -o "ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_rep/ENCFF558PHY_ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
4987 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46780
submission_time:            Thu Apr 13 12:49:46 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_pooled_rep.line_66.id_10.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 2
ID task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11
Name macs2 n/s ppr1
Thread thread_Root
PID 46781
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:49:46
End 2017-04-13 12:49:46
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1 -o "ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr1/ENCFF558PHY.pr1_ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
44579 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46781
submission_time:            Thu Apr 13 12:49:46 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_ppr1.line_66.id_11.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 3
ID task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12
Name macs2 n/s ppr2
Thread thread_Root
PID 46782
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:49:47
End 2017-04-13 12:49:47
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 213 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2 -o "ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pooled_pseudo_reps/ppr2/ENCFF558PHY.pr2_ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
4985 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46782
submission_time:            Thu Apr 13 12:49:47 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_ppr2.line_66.id_12.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 4
ID task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13
Name macs2 n/s rep1
Thread thread_Root
PID 46783
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:49:48
End 2017-04-13 12:49:48
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1 -o "ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1 -o "ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep1/ENCFF558PHY.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
44578 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46783
submission_time:            Thu Apr 13 12:49:48 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1.line_66.id_13.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 5
ID task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14
Name macs2 n/s rep1-pr1
Thread thread_Root
PID 46784
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:49:49
End 2017-04-13 12:49:49
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1 -o "ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr1/ENCFF558PHY.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
4986 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46784
submission_time:            Thu Apr 13 12:49:49 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1_pr1.line_66.id_14.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 6
ID task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15
Name macs2 n/s rep1-pr2
Thread thread_Root
PID 46785
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:50:03
End 2017-04-13 12:50:03
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 215 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2 -o "ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep1/pr2/ENCFF558PHY.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
5237 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46785
submission_time:            Thu Apr 13 12:50:03 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep1_pr2.line_66.id_15.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 7
ID task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16
Name macs2 n/s rep2
Thread thread_Root
PID 46786
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:50:04
End 2017-04-13 12:50:04
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ true == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2 -o "ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2 -o "ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/signal/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/rep2/ENCFF645WYX.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
45240 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46786
submission_time:            Thu Apr 13 12:50:04 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2.line_66.id_16.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 8
ID task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17
Name macs2 n/s rep2-pr1
Thread thread_Root
PID 46787
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:50:05
End 2017-04-13 12:50:05
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1 -o "ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr1/ENCFF645WYX.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
5236 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46787
submission_time:            Thu Apr 13 12:50:05 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2_pr1.line_66.id_17.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
scheduling info:            There are no messages available
Num 9
ID task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18
Name macs2 n/s rep2-pr2
Thread thread_Root
PID 46788
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus
Mem
Start 2017-04-13 12:50:06
End 2017-04-13 12:50:06
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Dependencies 
 
# SYS command. line 68

 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 69

 export LC_COLLATE=C

# SYS command. line 74

 macs2 callpeak -t /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.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/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 210 --keep-dup all -B --SPMR

# SYS command. line 77

 sort -k 8gr,8gr "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz

# SYS command. line 80

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.xls \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_peaks.narrowPeak \
			"/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_summits.bed

# SYS command. line 84

 if [[ false == "false" ]]; then \
			rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg; \
			TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi; \
			exit; \
		fi

# SYS command. line 94

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -m FE

# SYS command. line 97

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph

# SYS command. line 98

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_FE.bdg

# SYS command. line 101

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 102

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw

# SYS command. line 103

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.srt.bedgraph

# SYS command. line 109

 chipReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')

# SYS command. line 111

 controlReads=$(zcat /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')

# SYS command. line 113

 macs2 bdgcmp -t "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg -c "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg --outdir /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2 -o "ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"

# SYS command. line 116

 slopBed -i "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg -g /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes -b 0 |   awk '{if ($3 != -1) print $0}' |  bedClip stdin /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph

# SYS command. line 117

 rm -rf "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_ppois.bdg

# SYS command. line 120

 sort -k1,1 -k2,2n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 121

 bedGraphToBigWig /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph /mnt/data/bds_pipeline_genome_data/hg38/hg38.chrom.sizes /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw

# SYS command. line 122

 rm -f /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bedgraph /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.srt.bedgraph

# SYS command. line 124

 rm -f "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_treat_pileup.bdg "/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/peak/macs2/pseudo_reps/rep2/pr2/ENCFF645WYX.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign"_control_lambda.bdg

# SYS command. line 126

 TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
 
   
--------------------Stdout--------------------
5409 (process ID) old priority 0, new priority 19

 
--------------------Stderr--------------------
Traceback (most recent call last):
  File "/software/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in 
    __import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2991, in 
    @_call_aside
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2977, in _call_aside
    f(*args, **kwargs)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3004, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master
    ws = cls()
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 646, in __init__
    self.add_entry(entry)
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 702, in add_entry
    for dist in find_distributions(entry, True):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1996, in find_on_path
    path_item, entry, metadata, precedence=DEVELOP_DIST
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2405, in from_location
    py_version=py_version, platform=platform, **kw
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2746, in _reload_version
    md_version = _version_from_file(self._get_metadata(self.PKG_INFO))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2370, in _version_from_file
    line = next(iter(version_lines), '')
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2538, in _get_metadata
    for line in self.get_metadata_lines(name):
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1474, in get_metadata_lines
    return yield_lines(self.get_metadata(name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1470, in get_metadata
    value = self._get(self._fn(self.egg_info, name))
  File "/users/imk1/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1579, in _get
    with open(path, 'rb') as stream:
IOError: [Errno 13] Permission denied: '/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/httplib2-0.9.2-py2.7.egg-info/PKG-INFO'

 
--------------------Post mortem info--------------------
==============================================================
job_number:                 46788
exec_file:                  job_scripts/46788
submission_time:            Thu Apr 13 12:50:06 2017
owner:                      imk1
uid:                        1048
group:                      users
gid:                        100
sge_o_home:                 /users/imk1/
sge_o_log_name:             imk1
sge_o_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
sge_o_shell:                /bin/bash
sge_o_workdir:              /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2
sge_o_host:                 surya
account:                    sge
stderr_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18.stderr.cluster
mail_list:                  imk1@surya
notify:                     FALSE
job_name:                   STDIN
stdout_path_list:           NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/chipseq.bds.20170413_124933_982/task.callpeak_macs2.macs2_n_s_rep2_pr2.line_66.id_18.stdout.cluster
jobshare:                   0
env_list:                   LIBRARY_PATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/lib,TMUX=/tmp/tmux-1048/default,43619,2,MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 57066 22,USER=imk1,J2SDKDIR=/usr/lib/jvm/java-8-oracle,SHLVL=4,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5,J2REDIR=/usr/lib/jvm/java-8-oracle/jre,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift,SSH_TTY=/dev/pts/4,LOGNAME=imk1,_=/usr/bin/bds,EVENT_NOEPOLL=1,XDG_SESSION_ID=67062,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/users/imk1/.local/lib/python2.7/site-packages/keras/,SGE_ROOT=/var/lib/gridengine,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,DERBY_HOME=/usr/lib/jvm/java-8-oracle/db,PERL5LIB=/users/imk1/perl5/lib/perl5,XDG_RUNTIME_DIR=/run/user/1048,DISPLAY=localhost:12.0,SGE_CELL=default,STY=43698.ZIC2_MACS2.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_CCx82k,XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2,JAVA_HOME=/usr/lib/jvm/java-8-oracle,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 57067 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/users/imk1/.local/lib/python2.7/site-packages/keras/:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,CPATH=/users/imk1/anaconda2/pkgs/gsl-1.16-1/include,MODULEPATH=/usr/local/Modules/versions				:/usr/local/Modules/$MODULE_VERSION/modulefiles	:/modules/				:/software/modulefiles,TMUX_PANE=%2,MODULESHOME=/software/env_module/3.2.10
script_file:                STDIN
usage    1:                 cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info:            There are no messages available

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /usr/bin/bds
bool allowEmpty false
string[] args [-title, ZIC2_MACS2, -nth, 5, -species, hg38, -url_base, http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZIC2_MACS2/out, -filt_bam1, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep1/ENCFF558PHY.bam, -filt_bam2, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZIC2_MACS2/out/align/rep2/ENCFF645WYX.bam, -ctl_tag, /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz, -pe, -macs2_for_idr, $]
bool canFail false
string CPATH /users/imk1/anaconda2/pkgs/gsl-1.16-1/include
int cpus -1
int cpusLocal 56
int day 86400
string DEEPLIFT_DIR /srv/scratch/imk1/TFBindingPredictionProject/src/deeplift/deeplift
string DERBY_HOME /usr/lib/jvm/java-8-oracle/db
string DISPLAY localhost:12.0
real E 2.718281828459045
string ENHANCER_SCRIPTS_DIR /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/
string EVENT_NOEPOLL 1
int G 1073741824
string HOME /users/imk1/
int hour 3600
string J2REDIR /usr/lib/jvm/java-8-oracle/jre
string J2SDKDIR /usr/lib/jvm/java-8-oracle
string JAVA_HOME /usr/lib/jvm/java-8-oracle
int K 1024
string KERAS_DIR /users/imk1/.local/lib/python2.7/site-packages/keras/
string KRB5CCNAME FILE:/tmp/krb5cc_1048_CCx82k
string LANG en_US.UTF-8
string LIBRARY_PATH /users/imk1/anaconda2/pkgs/gsl-1.16-1/lib
string LOADEDMODULES
string LOGNAME imk1
int M 1048576
string MAIL /var/mail/imk1
int mem -1
int minute 60
string MODULE_VERSION 3.2.10
string MODULE_VERSION_STACK 3.2.10
string MODULEPATH /usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$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/ZIC2_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/ZIC2_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 43698.ZIC2_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