BigDataScript report: atac.bds

Script file /srv/scratch/annashch/bds_atac/atac.bds
Program ID atac.bds.20160516_125706_933
Start time 2016-05-16 12:57:06
Run time 13:16:48.538
Tasks executed 2
Tasks failed 2
Tasks failed names
bowtie2_PE rep1
bowtie2_PE rep2
Arguments* [-out_dir, /srv/scratch/annashch/sundari/output, -fastq1_1, output/align/rep1/160429-BW-1_R1.trim.fastq.gz, -fastq1_2, output/align/rep1/160429-BW-1_R2.trim.fastq.gz, -fastq2_1, output/align/rep2/160429-BW-2_R1.trim.fastq.gz, -fastq2_2, output/align/rep2/160429-BW-2_R2.trim.fastq.gz, -species, hg19, -pseudorep, -idr, -blacklist, /srv/scratch/annashch/refs/wgEncodeDacMapabilityConsensusExcludable.bed, -par_lvl, 5, -trimmed_fastq]
System* local
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
  
thread_20 thread_Root
 atac.bds.20160516_125706_933_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_128.id_6
 
thread_21 thread_Root
 atac.bds.20160516_125706_933_parallel_21/task.align_bowtie2.bowtie2_PE_rep2.line_128.id_7
 

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.align_bowtie2.bowtie2_PE_rep1.line_128.id_6
Name bowtie2_PE rep1
Thread thread_20
PID 41025
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 2
Mem
Start 2016-05-16 12:57:08
End 2016-05-16 12:57:08
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 /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 89 files...
[E::hts_open] fail to open file '/srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE.0054.bam'
[bam_merge_core] fail to open file /srv/scratch/annashch/sundari/output/align/rep1/160429-BW-1_R1.trim.PE2SE.0054.bam

 
Num 2
ID task.align_bowtie2.bowtie2_PE_rep2.line_128.id_7
Name bowtie2_PE rep2
Thread thread_21
PID 41030
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 2
Mem
Start 2016-05-16 12:57:08
End 2016-05-16 12:57:08
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 /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
[bam_sort_core] merging from 92 files...
[E::hts_open] fail to open file '/srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE.0049.bam'
[bam_merge_core] fail to open file /srv/scratch/annashch/sundari/output/align/rep2/160429-BW-2_R1.trim.PE2SE.0049.bam

 

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, output/align/rep1/160429-BW-1_R1.trim.fastq.gz, -fastq1_2, output/align/rep1/160429-BW-1_R2.trim.fastq.gz, -fastq2_1, output/align/rep2/160429-BW-2_R1.trim.fastq.gz, -fastq2_2, output/align/rep2/160429-BW-2_R2.trim.fastq.gz, -species, hg19, -pseudorep, -idr, -blacklist, /srv/scratch/annashch/refs/wgEncodeDacMapabilityConsensusExcludable.bed, -par_lvl, 5, -trimmed_fastq]
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 /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:/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:/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
int P 1125899906842624
string PATH /srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/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:/srv/scratch/annashch/deeplearning_avanti/exec:/users/annashch/keras:/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:/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:/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:/home/leepc12/.bds:/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/keras:/srv/scratch/annashch/Basset/src:/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 53764 22
string SSH_CONNECTION 10.39.35.84 53764 171.65.76.244 22
string SSH_TTY /dev/pts/17
string STY 40954.pts-17.nandi
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