Script file	/srv/scratch/annashch/bds_atac/atac.bds
Program ID	atac.bds.20160518_164836_185
Start time	2016-05-18 16:48:36
Run time	00:00:11.541
Tasks executed	3
Tasks failed	2
Tasks failed names	ataqc rep2 ataqc rep1
Arguments*	[-multimapping, 4, -out_dir, 4x_experiments/UnplacedChroms_multiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160518_164836_185/task.base.line_414.id_14
thread_20	thread_Root
thread_21	thread_Root
thread_41	thread_Root	atac.bds.20160518_164836_185_parallel_41/task.atac.ataqc_rep1.line_861.id_15
thread_42	thread_Root	atac.bds.20160518_164836_185_parallel_42/task.atac.ataqc_rep2.line_861.id_16

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.base.line_414.id_14
Name	task.base.line_414.id_14
Thread	thread_Root
PID	17757

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-05-18 16:48:38
End	2016-05-18 16:48:38
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz
Dependencies

 
# SYS command. line 416

 cp /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/pooled_pseudo_reps/ppr.IDR0.1.filt.narrowPeak.gz /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 417

 while [ ! -f /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz ]; do echo FOUND DELAYED WRITE, WAITING...; sleep 0.1; done

Num	2
ID	task.atac.ataqc_rep1.line_861.id_15
Name	ataqc rep1
Thread	thread_41
PID	17770

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	1
Mem

Start	2016-05-18 16:48:39
End	2016-05-18 16:48:39
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE_qc.html /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE_qc.txt
Dependencies

 
# SYS command. line 863

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 867

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 869

 cd /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1

# SYS command. line 871

 /srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
		    --workdir /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1 \
		    --outdir /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1 \
		    --outprefix 3hr_rep2_merged_R1.trim.PE2SE \
		    --genome hg19 \
		    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
		    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
		    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
		    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
		    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
		    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
		    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
		    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
		    --pbc /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.pbc.qc\
		    --fastq1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz --fastq2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz \
		    --alignedbam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam \
		    --alignmentlog /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.align.log \
		    --coordsortbam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.bam \
		    --duplog /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep1/3hr_rep2_merged_R1.trim.PE2SE.dup.qc \
		    --finalbam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam \
		    --finalbed /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
		    --bigwig /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
		    --peaks /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
		    --naive_overlap_peaks /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
		    --idr_peaks /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/annashch/anaconda2/bin from PATH
prepending /users/annashch/anaconda2/envs/bds_atac/bin to PATH
samtools: symbol lookup error: /lib/x86_64-linux-gnu/libncurses.so.5: undefined symbol: _nc_putchar
Traceback (most recent call last):
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1519, in 
    main()
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1308, in main
    paired_status = determine_paired(FINAL_BAM)
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 106, in determine_paired
    '-c', bam_file]).strip())
  File "/users/annashch/anaconda2/envs/bds_atac/lib/python2.7/subprocess.py", line 573, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['samtools', 'view', '-f', '0x1', '-c', '/srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.PE2SE.nodup.bam']' returned non-zero exit status 127

Num	3
ID	task.atac.ataqc_rep2.line_861.id_16
Name	ataqc rep2
Thread	thread_42
PID	17775

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	1
Mem

Start	2016-05-18 16:48:39
End	2016-05-18 16:48:39
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE_qc.html /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE_qc.txt
Dependencies

 
# SYS command. line 863

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/srv/scratch/annashch/bds_atac/.:/srv/scratch/annashch/bds_atac/modules:/srv/scratch/annashch/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds;

# SYS command. line 867

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 869

 cd /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2

# SYS command. line 871

 /srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py \
		    --workdir /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2 \
		    --outdir /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2 \
		    --outprefix 3hr_rep3_merged_R1.trim.PE2SE \
		    --genome hg19 \
		    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
		    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
		    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
		    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
		    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
		    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
		    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
		    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
		    --pbc /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.pbc.qc\
		    --fastq1 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz --fastq2 /srv/scratch/annashch/output/4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz \
		    --alignedbam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam \
		    --alignmentlog /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.align.log \
		    --coordsortbam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.bam \
		    --duplog /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/qc/rep2/3hr_rep3_merged_R1.trim.PE2SE.dup.qc \
		    --finalbam /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam \
		    --finalbed /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.tagAlign.gz \
		    --bigwig /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/signal/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
		    --peaks /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
		    --naive_overlap_peaks /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/macs2/overlap/3hr_rep2_merged_R1.trim.PE2SE.nodup.tn5_pooled.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
		    --idr_peaks /srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/peak/idr/optimal_set/ppr.IDR0.1.filt.narrowPeak.gz

    
--------------------Stderr--------------------
discarding /users/annashch/anaconda2/bin from PATH
prepending /users/annashch/anaconda2/envs/bds_atac/bin to PATH
samtools: symbol lookup error: /lib/x86_64-linux-gnu/libncurses.so.5: undefined symbol: _nc_putchar
Traceback (most recent call last):
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1519, in 
    main()
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 1308, in main
    paired_status = determine_paired(FINAL_BAM)
  File "/srv/scratch/annashch/bds_atac/ataqc/run_ataqc.py", line 106, in determine_paired
    '-c', bam_file]).strip())
  File "/users/annashch/anaconda2/envs/bds_atac/lib/python2.7/subprocess.py", line 573, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['samtools', 'view', '-f', '0x1', '-c', '/srv/scratch/annashch/output/4x_experiments/UnplacedChroms_multiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.PE2SE.nodup.bam']' returned non-zero exit status 127

Global scope

Note: Global scope when program finished execution.

Type	Name	Value
string	_	/bin/sh
string	_JAVA_OPTIONS	-Xms256M -Xmx512M -XX:ParallelGCThreads=1
bool	allowEmpty	false
string[]	args	[-multimapping, 4, -out_dir, 4x_experiments/UnplacedChroms_multiMap_3hr, -fastq1_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R1.trim.fastq.gz, -fastq1_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep1/3hr_rep2_merged_R2.trim.fastq.gz, -fastq2_1, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R1.trim.fastq.gz, -fastq2_2, 4x_experiments/baseChroms_noMultiMap_3hr/align/rep2/3hr_rep3_merged_R2.trim.fastq.gz, -bwt2_idx, /srv/scratch/annashch/refs/hg19_mm9_phix_filtered_with_unplaced_unlocalized, -gensz, hs, -chrsz, /srv/scratch/annashch/refs/hg19_mm9_phix_unplaced_chrom.sizes, -species, hg19, -pseudorep, -idr, -blacklist_idr, wgEncodeDacMapabilityConsensusExcludable.bed, -trimmed_fastq]
string	BASSETDIR	/srv/scratch/annashch/Basset
bool	canFail	false
int	cpus	1
int	cpusLocal	48
string	CRC	/srv/scratch/annashch/crc
int	day	86400
string	DEEPLEARN_SCRIPTS_DIR	/srv/scratch/annashch/deeplearning_avanti
string	DEEPLIFT_DIR	/srv/scratch/annashch/deeplift/deeplift
real	E	2.718281828459045
string	EIGEN	/mnt/lab_data/montgomery/shared/Eigen
string	ENHANCER_SCRIPTS_DIR	/srv/scratch/annashch/enhancer_prediction_code
int	G	1073741824
string	HOME	/users/annashch/
int	hour	3600
int	K	1024
string	KERAS_DIR	/users/annashch/keras
string	LANG	en_US.UTF-8
string	LD_LIBRARY_PATH	/lib/x86_64-linux-gnu:/usr/local/cudnn/lib64:
string	LOADEDMODULES
string	LOGNAME	annashch
string	LUACPATH	/srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
string	LUAPATH	/srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
int	M	1048576
string	MAIL	/var/mail/annashch
string	MALLOC_ARENA_MAX	4
string	MAX_JAVA_MEM	20G
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	node
int	P	1125899906842624
string	PATH	/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/users/annashch/keras:/users/annashch/anaconda2/bin:/users/annashch/anaconda2/lib:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/users/annashch/keras:/users/annashch/anaconda2/bin:/users/annashch/anaconda2/lib:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin
real	PI	3.141592653589793
string	ppwd	/srv/scratch/annashch/output
string	programName	atac.bds
string	programPath	/srv/scratch/annashch/bds_atac/atac.bds
string	PWD	/srv/scratch/annashch/output
string	PYTHONPATH	/users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/anaconda2/bin:/users/annashch/anaconda2/lib:/users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/keras:/srv/scratch/annashch/Basset/src:/users/annashch/anaconda2/bin:/users/annashch/anaconda2/lib:/users/annashch/keras:/srv/scratch/annashch/Basset/src:
string	QT_QPA_PLATFORMTHEME	appmenu-qt5
string	queue
int	retry	0
string	SHELL	/bin/bash
string	SHLVL	2
string	SSH_CLIENT	10.0.2.3 50999 22
string	SSH_CONNECTION	10.0.2.3 50999 10.0.2.8 22
string	SSH_TTY	/dev/pts/136
string	STY	17678.pts-136.kali
string	system	local
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#57:co#205: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:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{\|\|}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:Km=\\E[M:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:\\\n\t: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:F3=\\E[1;2P:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:\\\n\t:F7=\\E[15;2~:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=:\\\n\t:K2=\\EOE:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:4=\\E[3;2~:\\\n\t:7=\\E[1;2F:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:\\\n\t:%e=\\E[5;2~:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:\\\n\t:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:\\\n\t:kd=\\EOB:kr=\\EOC:kl=\\EOD:km:
int	timeout	-1
string	USER	annashch
string	UTIL_SCRIPTS_DIR	/srv/scratch/annashch/av_scripts
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XDG_RUNTIME_DIR	/run/user/1091
string	XDG_SESSION_ID	936

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope