Script file	/srv/scratch/annashch/bds_atac/atac.bds
Program ID	atac.bds.20160516_092027_240
Start time	2016-05-16 09:20:27
Run time	02:37:12.115
Tasks executed	4
Tasks failed	2
Tasks failed names	bowtie2_PE rep1 bowtie2_PE rep2
Arguments*	[-out_dir, /srv/scratch/annashch/sundari/output, -fastq1_1, /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R1.fastq, -fastq1_2, /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R2.fastq, -fastq2_1, /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R1.fastq, -fastq2_2, /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R2.fastq, -species, hg19, -pseudorep, -idr, -blacklist, /srv/scratch/annashch/refs/wgEncodeDacMapabilityConsensusExcludable.bed, -par_lvl, 5]
System*	local
Cpus*	1
Exit value	1

Thread ID	Parent	Tasks
thread_Root	None
thread_20	thread_Root	atac.bds.20160516_092027_240_parallel_20/task.align_etc.trim_adapters_PE_rep1.line_57.id_6 atac.bds.20160516_092027_240_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_128.id_8
thread_21	thread_Root	atac.bds.20160516_092027_240_parallel_21/task.align_etc.trim_adapters_PE_rep2.line_57.id_7 atac.bds.20160516_092027_240_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_128.id_9

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_etc.trim_adapters_PE_rep1.line_57.id_6
Name	trim_adapters_PE rep1
Thread	thread_20
PID	2423

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

Start	2016-05-16 09:20:28
End	2016-05-16 11:46:21
Elapsed	02:25:53
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R1.fastq /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R2.fastq
Output files	/srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.fastq.gz /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R2.trim.fastq.gz
Dependencies

 
# SYS command. line 59

 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 61

 cd /srv/scratch/annashch/sundari/output/align/rep1

# SYS command. line 62

 $(which trimAdapters.py) -a /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R1.fastq -b /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R2.fastq

# SYS command. line 63

 gzip /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.fastq

# SYS command. line 64

 gzip /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R2.trim.fastq

   
--------------------Stdout--------------------
160429-BW-1_R1.trim.fastq
160429-BW-1_R2.trim.fastq

 
--------------------Stderr--------------------
discarding /users/annashch/anaconda2/bin from PATH
prepending /users/annashch/anaconda2/envs/bds_atac/bin to PATH
109071066 sequences total
47754455 sequences trimmed with 0 mismatches
1491158 sequences trimmed with 1 mismatch
24 mean number of bases trimmed for reads requiring trimming

Num	2
ID	task.align_etc.trim_adapters_PE_rep2.line_57.id_7
Name	trim_adapters_PE rep2
Thread	thread_21
PID	2429

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

Start	2016-05-16 09:20:28
End	2016-05-16 11:57:35
Elapsed	02:37:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R1.fastq /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R2.fastq
Output files	/srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.fastq.gz /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R2.trim.fastq.gz
Dependencies

 
# SYS command. line 59

 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 61

 cd /srv/scratch/annashch/sundari/output/align/rep2

# SYS command. line 62

 $(which trimAdapters.py) -a /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R1.fastq -b /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R2.fastq

# SYS command. line 63

 gzip /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.fastq

# SYS command. line 64

 gzip /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R2.trim.fastq

   
--------------------Stdout--------------------
160429-BW-2_R1.trim.fastq
160429-BW-2_R2.trim.fastq

 
--------------------Stderr--------------------
discarding /users/annashch/anaconda2/bin from PATH
prepending /users/annashch/anaconda2/envs/bds_atac/bin to PATH
111904547 sequences total
45583785 sequences trimmed with 0 mismatches
1526129 sequences trimmed with 1 mismatch
23 mean number of bases trimmed for reads requiring trimming

Num	3
ID	task.align_bowtie2.bowtie2_PE_rep1.line_128.id_8
Name	bowtie2_PE rep1
Thread	thread_20
PID	38007

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	2
Mem

Start	2016-05-16 11:46:22
End	2016-05-16 11:46:22
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.fastq.gz /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R2.trim.fastq.gz
Output files	/srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE.bam /srv/scratch/annashch/sundari/output/qc/rep1/160429-BW-1_R1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 130

 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 134

 bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.fastq.gz -2 /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R2.trim.fastq.gz 2>/srv/scratch/annashch/sundari/output/qc/rep1/160429-BW-1_R1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE

# SYS command. line 137

 samtools index /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE.bam

    
--------------------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
samtools: symbol lookup error: /lib/x86_64-linux-gnu/libncurses.so.5: undefined symbol: _nc_putchar

Num	4
ID	task.align_bowtie2.bowtie2_PE_rep2.line_128.id_9
Name	bowtie2_PE rep2
Thread	thread_21
PID	38839

OK	false
Exit Code	1
Retries
State	ERROR
Dep.	ERROR
Cpus	2
Mem

Start	2016-05-16 11:57:36
End	2016-05-16 11:57:36
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.fastq.gz /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R2.trim.fastq.gz
Output files	/srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE.bam /srv/scratch/annashch/sundari/output/qc/rep2/160429-BW-2_R1.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 130

 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 134

 bowtie2 -X2000 --mm --threads 2 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.fastq.gz -2 /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R2.trim.fastq.gz 2>/srv/scratch/annashch/sundari/output/qc/rep2/160429-BW-2_R1.trim.PE2SE.align.log | samtools view -bS - | samtools sort - /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE

# SYS command. line 137

 samtools index /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE.bam

    
--------------------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
samtools: symbol lookup error: /lib/x86_64-linux-gnu/libncurses.so.5: undefined symbol: _nc_putchar

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	[-out_dir, /srv/scratch/annashch/sundari/output, -fastq1_1, /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R1.fastq, -fastq1_2, /mnt/lab_data/kundaje/projects/sundari/160429-BW-1_R2.fastq, -fastq2_1, /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R1.fastq, -fastq2_2, /mnt/lab_data/kundaje/projects/sundari/160429-BW-2_R2.fastq, -species, hg19, -pseudorep, -idr, -blacklist, /srv/scratch/annashch/refs/wgEncodeDacMapabilityConsensusExcludable.bed, -par_lvl, 5]
string	BASSETDIR	/srv/scratch/annashch/Basset
bool	canFail	false
string	CONFIG_PATH	/etc/default/gridengine
int	cpus	1
int	cpusLocal	48
string	CRC	/srv/scratch/annashch/crc
string	CUDA_ROOT	/usr/local/cuda
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	/usr/local/cudnn/lib64:/usr/local/cudnn/lib64:
string	LOADEDMODULES
string	LOGNAME	annashch
string	LUACPATH	/srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:/srv/scratch/annashch/Basset/src:
string	LUAPATH	/srv/scratch/annashch/Basset/src:/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	NCBI_VDB_LIBDIR	/usr/local/ncbi/ncbi-vdb/lib64
string	NGS_LIBDIR	/usr/local/ngs/ngs-sdk/lib64
string	node
string	OLDPWD	/srv/scratch/annashch/stemcells/het/output
int	P	1125899906842624
string	PATH	/srv/scratch/annashch/deeplearning_avanti/exec:/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/anaconda2/bin:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/users/annashch/anaconda2/bin:/users/annashch/torch/install/bin/:/srv/scratch/annashch/Basset:/usr/local/ncbi/sra-tools/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/leepc12/.bds:/software/miniconda3/bin:/users/annashch//.bds:/users/annashch/bowtie2-2.2.9:/usr/local/cuda/bin:/home/leepc12/.bds:/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/sundari
string	programName	atac.bds
string	programPath	/srv/scratch/annashch/bds_atac/atac.bds
string	PWD	/srv/scratch/annashch/sundari
string	PYTHONPATH	/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/keras:/srv/scratch/annashch/Basset/src:
string	queue
int	retry	0
string	SGE_CELL	default
string	SGE_ROOT	/var/lib/gridengine
string	SHELL	/bin/bash
string	SHLVL	2
string	SSH_CLIENT	10.39.35.84 60414 22
string	SSH_CONNECTION	10.39.35.84 60414 171.65.76.244 22
string	SSH_TTY	/dev/pts/55
string	STY	20579.3hr_rep1
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

BigDataScript report: atac.bds

Timeline

Task Graph

Parallel (threads) details

Task details

Global scope