Num | 1 | ID | task.align_bwa.bwa_sam_rep1.line_140.id_10 | Name | bwa_sam rep1 | Thread | thread_41 | PID | 165 | | OK | false | Exit Code | 1 | Retries | | State | ERROR | Dep. | ERROR | Cpus | 4 | Mem | | | Start | 2016-10-09 13:36:27 | End | 2016-10-09 13:36:27 | Elapsed | 00:00:00 | Timeout | 00:00:-1 | Wall Timeout | 100 days | | Input files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/R339W_allReps.fastq.gz
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.sai
| Output files | /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.bam
/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/rep1/R339W_allReps.flagstat.qc
| Dependencies | | |
# SYS command. line 142
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; fi; export PATH=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/.:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/modules:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/src/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s); renice -n 10 $$
# SYS command. line 147
bwa samse /mnt/data/annotations/by_organism/mouse/mm10/indices/mm10_male_bwa0.7.10/genome.fa /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.sai /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/RawReads/R339W_allReps.fastq.gz | samtools view -Su /dev/stdin \
| sambamba sort -t 4 /dev/stdin -o /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.bam
# SYS command. line 149
sambamba flagstat -t 4 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/align/rep1/R339W_allReps.bam > /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/out/qc/rep1/R339W_allReps.flagstat.qc
# SYS command. line 151
TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; fi
--------------------Stdout--------------------
8096 (process ID) old priority 0, new priority 10
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/aquas_chipseq/bin to PATH
[bwa_read_seq] 0.5% bases are trimmed.
[bwa_aln_core] convert to sequence coordinate... [samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
--------------------Post mortem info--------------------
==============================================================
job_number: 165
exec_file: job_scripts/165
submission_time: Sun Oct 9 13:36:27 2016
owner: imk1
uid: 1048
group: users
gid: 100
sge_o_home: /users/imk1/
sge_o_log_name: imk1
sge_o_path: /users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/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:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect
sge_o_shell: /bin/bash
sge_o_workdir: /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W
sge_o_host: surya
account: sge
stderr_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/chipseq.bds.20161009_133624_466_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_10.stderr.cluster
mail_list: imk1@surya
notify: FALSE
job_name: STDIN
stdout_path_list: NONE:NONE:/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W/chipseq.bds.20161009_133624_466_parallel_41/task.align_bwa.bwa_sam_rep1.line_140.id_10.stdout.cluster
jobshare: 0
env_list: MAIL=/var/mail/imk1,SSH_CLIENT=171.65.77.8 51178 22,USER=imk1,SHLVL=3,PERL_LOCAL_LIB_ROOT=/users/imk1/perl5:/users/imk1/perl5,HOME=/users/imk1/,DEEPLIFT_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/deeplift_private/deeplift,SSH_TTY=/dev/pts/18,LOGNAME=imk1,_=/usr/bin/bds,TERM=screen,PERL_MB_OPT=--install_base "/users/imk1/perl5",KERAS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/keras,SGE_ROOT=/var/lib/gridengine,PATH=/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/imk1/TFBindingPredictionProject/src/rcade/:/users/imk1/perl5/bin:/srv/scratch/imk1/TFBindingPredictionProject/src/bedtools2/bin:/usr/local/cuda/bin:/srv/persistent/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:/users/imk1/edirect:/users/imk1/edirect:/users/imk1/edirect,PERL5LIB=/users/imk1/perl5/lib/perl5:/users/imk1/perl5/lib/perl5,DISPLAY=localhost:12.0,SGE_CELL=default,STY=29979.R339W.BDS,LANG=en_US.UTF-8,SHELL=/bin/bash,KRB5CCNAME=FILE:/tmp/krb5cc_1048_rUZelg,RULEFITBASE=/srv/scratch/imk1/TFBindingPredictionProject/src/RuleFit/,PERL_MM_OPT=INSTALL_BASE=/users/imk1/perl5,UTIL_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/av_scripts/,MODULE_VERSION=3.2.10,MODULE_VERSION_STACK=3.2.10,WINDOW=0,PWD=/srv/scratch/shared/surya/imk1/TFBindingPredictionProject/MouseMutantData/R339W,LOADEDMODULES=NONE,SSH_CONNECTION=171.65.77.8 51178 171.65.76.63 22,TERMCAP=SC|screen|VT 100/ANSI X3.64 virtual terminal:\,PYTHONPATH=/software/python_anaconda/2.2.0/bin/python:/srv/scratch/imk1/TFBindingPredictionProject/src/pybedtools/,ENHANCER_SCRIPTS_DIR=/srv/scratch/imk1/TFBindingPredictionProject/src/enhancer_prediction_code/,MODULEPATH=/usr/local/Modules/versions :/usr/local/Modules/$MODULE_VERSION/modulefiles :/modules/ :/software/modulefiles,MODULESHOME=/software/env_module/3.2.10
script_file: STDIN
parallel environment: shm range: 4
usage 1: cpu=00:00:00, mem=0.00000 GBs, io=0.00000, vmem=N/A, maxvmem=N/A
scheduling info: queue instance "q@mitra" dropped because it is temporarily not available
queue instance "amd.q@mitra" dropped because it is temporarily not available
queue instance "q@amold" dropped because it is overloaded: np_load_avg=2.031563 (= 2.031563 + 0.50 * 0.000000 with nproc=32) >= 1.75
queue instance "amd.q@amold" dropped because it is overloaded: np_load_avg=2.031563 (= 2.031563 + 0.50 * 0.000000 with nproc=32) >= 1.75
queue instance "q@kali" dropped because it is full
queue instance "q@wotan" dropped because it is full
queue instance "amd.q@surya" dropped because it is full
queue instance "amd.q@kadru" dropped because it is full
queue instance "amd.q@kali" dropped because it is full
queue instance "amd.q@nandi" dropped because it is full
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