BigDataScript report: chipseq.bds

Script file /mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/chipseq.bds
Program ID chipseq.bds.20210825_232031_608
Start time 2021-08-25 23:20:31
Run time 00:00:13.238
Tasks executed 2
Tasks failed 2
Tasks failed names 
dedup_bam_PE_1 ctl1
dedup_bam_PE_1 rep1
Arguments* [-type, histone, -out_dir, /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD, -title, hd_h5, -pe, -species, galGal5, -system, local, -nth, 23, -bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam, -ctl_bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam]
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_38 thread_Root 
 chipseq.bds.20210825_232031_608_parallel_38/task.postalign_bam.dedup_bam_PE_1_rep1.line_278.id_11
thread_39 thread_Root 
 chipseq.bds.20210825_232031_608_parallel_39/task.postalign_bam.dedup_bam_PE_1_ctl1.line_278.id_10

Task details

Task Execution Time Dependencies Task program, Errors, StdOut / StdErr
Num 1
ID task.postalign_bam.dedup_bam_PE_1_ctl1.line_278.id_10
Name dedup_bam_PE_1 ctl1
Thread thread_39
PID 6464
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 11
Mem
Start 2021-08-25 23:20:34
End 2021-08-25 23:20:34
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam
Output files /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.filt.bam
Dependencies 
 
# SYS command. line 280

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 296

 if [[ 0 > 0 ]]; then \
				samtools view -F 524 -f 2 -u /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam | \
				sambamba sort -t 11 -n /dev/stdin -o /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam; \
				samtools view -h /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam | \
				$(which assign_multimappers.py) -k 0 --paired-end | \
				samtools fixmate -r /dev/stdin /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam.fixmate.bam; \
			    else \
			    	samtools view -F 1804 -f 2 -q 30 -u /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam | \
			    	sambamba sort -t 11 -n /dev/stdin -o /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam; \
			        samtools fixmate -r /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam.fixmate.bam; \
			    fi

# SYS command. line 308

 samtools view -F 1804 -f 2 -u /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam.fixmate.bam | sambamba sort -t 11 /dev/stdin -o /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.filt.bam

# SYS command. line 310

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam.fixmate.bam

# SYS command. line 311

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/ctl1/HD3_II_contrl.sort.dupmark.bam

# SYS command. line 313

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
 
    
--------------------Stderr--------------------
[E::hts_open] fail to open file '/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam'
samtools: failed to open "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam" for reading: Permission denied
sambamba-sort: not enough data in stream
Num 2
ID task.postalign_bam.dedup_bam_PE_1_rep1.line_278.id_11
Name dedup_bam_PE_1 rep1
Thread thread_38
PID 6479
OK false
Exit Code 1
Retries
State ERROR
Dep. ERROR
Cpus 12
Mem
Start 2021-08-25 23:20:35
End 2021-08-25 23:20:35
Elapsed 00:00:00
Timeout 00:00:-1
Wall Timeout 100 days
Input files /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam
Output files /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.filt.bam
Dependencies 
 
# SYS command. line 280

 if [[ -f $(which /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda) && $(/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin/activate aquas_chipseq; sleep 5; fi;  export PATH=/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/.:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/modules:/mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 296

 if [[ 0 > 0 ]]; then \
				samtools view -F 524 -f 2 -u /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam | \
				sambamba sort -t 12 -n /dev/stdin -o /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam; \
				samtools view -h /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam | \
				$(which assign_multimappers.py) -k 0 --paired-end | \
				samtools fixmate -r /dev/stdin /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam.fixmate.bam; \
			    else \
			    	samtools view -F 1804 -f 2 -q 30 -u /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam | \
			    	sambamba sort -t 12 -n /dev/stdin -o /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam; \
			        samtools fixmate -r /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam.fixmate.bam; \
			    fi

# SYS command. line 308

 samtools view -F 1804 -f 2 -u /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam.fixmate.bam | sambamba sort -t 12 /dev/stdin -o /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.filt.bam

# SYS command. line 310

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam.fixmate.bam

# SYS command. line 311

 rm -f /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD/align/rep1/HD3_II_rep1.sort.dupmark.bam

# SYS command. line 313

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
 
    
--------------------Stderr--------------------
[E::hts_open] fail to open file '/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam'
samtools: failed to open "/mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam" for reading: Permission denied
sambamba-sort: not enough data in stream

Global scope

Note: Global scope when program finished execution.
Type Name Value
string _ /mnt/storage/home/psbelokopytova/insulatory_index/.bds/bds
string _LMFILES_ /opt/shared/modules/jre/1.8.0
string _ModuleTable001_ 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
string _ModuleTable002_ Yi9tb2R1bGVmaWxlczovdXNyL3NoYXJlL2xtb2QvbW9kdWxlZmlsZXM6L29wdC9zaGFyZWQvbW9kdWxlcyIsfQ==
string _ModuleTable_Sz_ 2
bool allowEmpty false
string ALSA_CONFIG_PATH /etc/alsa-pulse.conf
string ANSOFT_LICENSE_FILE 1055@vm-ansys
string ANSYSLMD_LICENSE_FILE 1055@vm-ansys
string[] args [-type, histone, -out_dir, /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD, -title, hd_h5, -pe, -species, galGal5, -system, local, -nth, 23, -bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_rep1.sort.bam, -ctl_bam1, /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/Chickseq/HD3_II_contrl.sort.bam]
string AUDIODRIVER pulseaudio
string BASH_ENV /usr/share/lmod/7.6.1/init/bash
string BASH_FUNC_mc%% () { . /usr/share/mc/mc-wrapper.sh\n}
string BASH_FUNC_ml%% () { eval $($LMOD_DIR/ml_cmd \"$@\")\n}
string BASH_FUNC_module%% () { eval $($LMOD_CMD bash \"$@\") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)\n}
bool canFail false
string COLORTERM 1
string CPU x86_64
int cpus -1
int cpusLocal 24
string CSHEDIT emacs
string CVS_RSH ssh
int day 86400
real E 2.718281828459045
string ENVIRONMENT BATCH
string FROM_HEADER
string ftp_proxy http://proxy.hpc.nusc.ru:8080
int G 1073741824
string G_BROKEN_FILENAMES 1
string G_FILENAME_ENCODING @locale,UTF-8,ISO-8859-15,CP1252
string gopher_proxy
string GPG_TTY not a tty
string HISTSIZE 1000
string HOME /mnt/storage/home/psbelokopytova
string HOST cn303
string HOSTNAME cn303
string HOSTTYPE x86_64
int hour 3600
string http_proxy http://proxy.hpc.nusc.ru:8080
string https_proxy http://proxy.hpc.nusc.ru:8080
string INPUTRC /mnt/storage/home/psbelokopytova/.inputrc
string INTEL_LICENSE_FILE 28519@hpc-suvir1,28519@hpc-suvir2,28519@srpo
string JAVA_HOME /opt/shared/java/jre1.8.0_45
int K 1024
string LANG en_US.UTF-8
string LESS -M -I -R
string LESS_ADVANCED_PREPROCESSOR no
string LESSCLOSE lessclose.sh %s %s
string LESSKEY /etc/lesskey.bin
string LESSOPEN lessopen.sh %s
string LMOD_CMD /usr/share/lmod/lmod/libexec/lmod
string LMOD_COLORIZE no
string LMOD_DIR /usr/share/lmod/lmod/libexec
string LMOD_FULL_SETTARG_SUPPORT no
string LMOD_PKG /usr/share/lmod/lmod
string LMOD_PREPEND_BLOCK normal
string LMOD_SETTARG_CMD :
string LMOD_VERSION 7.6.1
string LOADEDMODULES jre/1.8.0
string LOGNAME psbelokopytova
int M 1048576
string MACHTYPE x86_64-suse-linux
string MAIL /var/spool/mail/psbelokopytova
string MANPATH /usr/local/man:/usr/local/share/man:/usr/share/man:/usr/man:/opt/pbs/share/man
int mem -1
string MINICOM -c on
int minute 60
string MLM_LICENSE_FILE 27000@hpc-suvir1,27000@hpc-suvir2,27000@srpo
string MODULEPATH /opt/ohpc/pub/modulefiles:/usr/share/lmod/modulefiles:/opt/shared/modules
string MODULESHOME /usr/share/lmod/lmod
string MORE -sl
string MSC_LICENSE_FILE 1700@hpc-suvir1,1700@hpc-suvir2,1700@srpo
string NCPUS 24
string NLSPATH /usr/dt/lib/nls/msg/%L/%N.cat
string NNTPSERVER news
string NO_PROXY localhost, 127.0.0.1, hpc.nusc.ru
string no_proxy localhost, 127.0.0.1, hpc.nusc.ru
string node
string OMP_NUM_THREADS 24
string OSTYPE linux
int P 1125899906842624
string PAGER less
string PATH /opt/shared/java/jre1.8.0_45/bin:/mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin:/mnt/storage/home/psbelokopytova/bin:/mnt/storage/home/psbelokopytova/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/opt/shared/bin:/opt/pbs/bin:/mnt/storage/home/psbelokopytova/insulatory_index/.bds
string PBS_ENVIRONMENT PBS_BATCH
string PBS_JOBCOOKIE 2E49413063B5B73A1BDEA11B45073275
string PBS_JOBDIR /mnt/storage/home/psbelokopytova
string PBS_JOBID 3520646.vm-pbs
string PBS_JOBNAME aquas_hd_h5.sh
string PBS_MOMPORT 15003
string PBS_NODEFILE /var/spool/pbs/aux/3520646.vm-pbs
string PBS_NODENUM 0
string PBS_O_HOME /mnt/storage/home/psbelokopytova
string PBS_O_HOST clu.hpc.nusc.ru
string PBS_O_LANG en_US.UTF-8
string PBS_O_LOGNAME psbelokopytova
string PBS_O_MAIL /var/mail/psbelokopytova
string PBS_O_PATH /mnt/storage/home/psbelokopytova/insulatory_index/miniconda3/bin:/mnt/storage/home/psbelokopytova/bin/:/mnt/storage/home/psbelokopytova/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/shared/bin:/opt/pbs/bin:/mnt/storage/home/psbelokopytova/insulatory_index/.bds/
string PBS_O_QUEUE xl230g9q
string PBS_O_SHELL /bin/bash
string PBS_O_SYSTEM Linux
string PBS_O_WORKDIR /mnt/storage/home/psbelokopytova/insulatory_index/bds_pipeline_genome_data/Chicken
string PBS_QUEUE xl230g9_middle
string PBS_TASKNUM 1
real PI 3.141592653589793
string ppwd /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD
string PROFILEREAD true
string programName chipseq.bds
string programPath /mnt/storage/home/psbelokopytova/insulatory_index/TF_chipseq_pipeline/chipseq.bds
string PWD /mnt/scratch/ws/manuriddinov/202109231429EVL24/Vertebrates/Chicken/HD
string PYTHONSTARTUP /etc/pythonstart
string QEMU_AUDIO_DRV pa
string QT_SYSTEM_DIR /usr/share/desktop-data
string queue
int retry 0
string SDL_AUDIODRIVER pulse
string SHELL /bin/bash
string SHLVL 3
string SOCKS5_SERVER
string SOCKS_PROXY
string socks_proxy
string system local
int T 1099511627776
int timeout -1
string TMPDIR /var/tmp/pbs.3520646.vm-pbs
string TZ Asia/Novosibirsk
string USER psbelokopytova
int walltimeout 8640000
int week 604800
string WINDOWMANAGER env GNOME_SHELL_SESSION_MODE=classic SLE_CLASSIC_MODE=1 gnome-session --session gnome-classic
string XCURSOR_THEME DMZ
string XDG_CONFIG_DIRS /etc/xdg
string XDG_DATA_DIRS /usr/share
string XFILESEARCHPATH /usr/dt/app-defaults/%L/Dt
string XKEYSYMDB /usr/X11R6/lib/X11/XKeysymDB
string XNLSPATH /usr/share/X11/nls