Started at Thu Oct  1 06:17:23 2020
Terminated at Thu Oct  1 06:19:29 2020
Results reported at Thu Oct  1 06:19:29 2020

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
#!/usr/bin/env bash

# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# VirtualFlow is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with VirtualFlow.  If not, see <https://www.gnu.org/licenses/>.

# LSF Settings
###############################################################################

#BSUB -J c-1.1
#BSUB -W 01:00
#BSUB -n 1
#BSUB -q voight_normal
#BSUB -oo ../workflow/output-files/jobs/job-1.1_%J.out           # File to which standard out will be written
#BSUB -wt '5'
#BSUB -wa 'USR1'

# Job Information
##################################################################################
echo
echo "                    *** Job Information ***                    "
echo "==============================================================="
echo
echo "Environment variables"
echo "------------------------"
env
echo
echo
echo "Job infos by bjobs"
echo "------------------------"
bjobs $LSB_JOBID

# Running the Job - Screening of the Ligands
######################################################################
echo
echo "                    *** Job Output ***                    "
echo "==========================================================="

(... more ...)
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time :                                   1.04 sec.
    Max Memory :                                 2 MB
    Average Memory :                             2.00 MB
    Total Requested Memory :                     -
    Delta Memory :                               -
    Max Swap :                                   -
    Max Processes :                              5
    Max Threads :                                6
    Run time :                                   126 sec.
    Turnaround time :                            126 sec.

The output (if any) follows:

                    *** Job Information ***                    
===============================================================

Environment variables
------------------------
MODULE_VERSION_STACK=3.2.10
MANPATH=/appl/git-2.5.0/share/man:/appl/vcftools-0.1.12b/man:/appl/emacs-24.3/share/man:/appl/mysql-5.6.17/man:/appl/gnuplot-4.6.5/share/man:/appl/python-3.6.5/man:/appl/perl-5.20.2/
man:/appl/R-3.6.1/man:/appl/OpenBUGS-3.2.3/share/man:/appl/JAGS-4.3.0/man:/appl/lapack-3.8.0/man:/appl/curl-7.37.0/share/man:/appl/gsl-2.5/share/man:/appl/openmpi-1.8.3/share/man:/ap
pl/python-2.7.14/man:/appl/gcc-4.9.4/man:/lsf/10.1/man:
LSB_EXEC_CLUSTER=PMACS-SCC
HOSTNAME=devastator
LSB_EFFECTIVE_RSRCREQ=select[type == local] order[r15s:pg] 
LSF_LIM_API_NTRIES=1
LSF_LOGDIR=/lsf/log
LSB_BATCH_JID=6946271
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=72.78.190.137 52378 22
PERL5LIB=/appl/vcftools-0.1.12b/perl:/appl/perl-5.20.2/lib/5.20.2
LS_EXECCWD=/project/voight_ML/thomc/thomc_results/VirtualFlow/VFLP/VFLP-trial/tools
LSB_TRAPSIGS=trap # 15 10 12 2 1
LS_JOBPID=35378
LSB_JOBRES_CALLBACK=50942@devastator
VF_VERBOSITY_COMMANDS=standard
LSB_MAX_NUM_PROCESSORS=1
LSB_JOB_EXECUSER=thomc
VF_CONTROLFILE=../workflow/control/all.ctrl
LSF_SERVERDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/etc
LSB_JOBID=6946271
LSB_JOBRES_PID=35378
SSH_TTY=/dev/pts/14
LAPACKE_INCLUDE_DIR=/appl/lapack-3.8.0/include
LSB_JOBNAME=c-1.1
BSUB_BLOCK_EXEC_HOST=
LSF_LIBDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/lib
LSB_PROJECT_NAME=default
EXTRA_LINK_DIRECTORY=/appl/gsl-2.5/include
USER=thomc
LD_LIBRARY_PATH=/lsf/10.1/linux3.10-glibc2.17-x86_64/lib:/appl/git-2.5.0/lib:/appl/vcftools-0.1.12b/lib:/appl/bamtools-2.3.0/lib:/appl/mysql-5.6.17/lib:/appl/python-3.6.5/lib:/appl/p
erl-5.20.2/lib:/appl/R-3.6.1/lib:/appl/R-3.6.1/lib64/R/lib:/appl/OpenBUGS-3.2.3/lib:/appl/JAGS-4.3.0/lib64:/appl/lapack-3.8.0/lib64:/appl/curl-7.37.0/lib:/appl/gmp-6.0.0/lib:/appl/mp
fr-3.1.2/lib:/appl/mpc-1.0.2/lib:/appl/gsl-2.5/lib:/appl/openmpi-1.8.3/lib:/appl/python-2.7.14/lib:/appl/gcc-4.9.4/lib64:/appl/gcc-4.9.4/lib:/lsf/10.1/linux2.6-glibc2.3-x86_64/lib
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;
5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lh
a=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5
;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9
:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=
38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mp
eg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.
rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.ax
v=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.r
a=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
SBD_KRB5CCNAME_VAL=
LD_LIBRARY_PATH_64=/appl/python-3.6.5/lib
LSB_EEXEC_REAL_UID=
QUEUE=voight
CPATH=/appl/bamtools-2.3.0/include:/appl/python-3.6.5/include:/appl/JAGS-4.3.0/include:/appl/gmp-6.0.0/include:/appl/mpfr-3.1.2/include:/appl/mpc-1.0.2/include:/appl/gsl-2.5/include/
gsl:/appl/gsl-2.5/include/:/appl/openmpi-1.8.3/include:/appl/python-2.7.14/include:/appl/gcc-4.9.4/include
HOSTTYPE=X86_64
LSF_INVOKE_CMD=bsub
LS_EXEC_T=START
LS_SUBCWD=/project/voight_ML/thomc/thomc_results/VirtualFlow/VFLP/VFLP-trial/tools
LSF_VERSION=34
LSB_UNIXGROUP_INT=thomc
LSB_HOSTS=devastator
LSB_JOBFILENAME=/home/thomc/.lsbatch/1601547443.6946271
MAIL=/var/spool/mail/thomc
PATH=/lsf/10.1/linux3.10-glibc2.17-x86_64/bin:/appl/qvina-2.0/bin:/usr/local/bin:/lsf/10.1/linux3.10-glibc2.17-x86_64/etc:/usr/local/bin:/appl/vftools-1.0/bin:/appl/plink-1.07:/appl/
STAR-2.5.1b/bin/:/appl/git-2.5.0/bin:/appl/vcftools-0.1.12b/bin:/appl/bedtools2-2.25.0/bin:/appl/annovar-2019Oct24:/appl/bamtools-2.3.0/bin:/appl/emacs-24.3/bin:/appl/mysql-5.6.17/bi
n:/appl/liftOver-20180423/bin:/appl/gnuplot-4.6.5/bin:/appl/python-3.6.5/bin:/appl/perl-5.20.2/bin:/appl/R-3.6.1/bin:/appl/OpenBUGS-3.2.3/bin:/appl/JAGS-4.3.0/bin:/appl/lapack-3.8.0/
bin:/appl/curl-7.37.0/bin:/appl/gsl-2.5/bin:/appl/openmpi-1.8.3/bin:/appl/python-2.7.14/bin:/appl/gcc-4.9.4/bin:/usr/local/bin:/lsf/10.1/linux2.6-glibc2.3-x86_64/etc:/lsf/10.1/linux2
.6-glibc2.3-x86_64/bin:/usr/local/bin:/usr/local/bin:/bin:/usr/bin
LSB_JOBINDEX=0
MODULE_VERSION=3.2.10
CUDA_VISIBLE_DEVICES_ORIG=
LSB_EXIT_PRE_ABORT=99
LSB_JOBEXIT_STAT=0
C_INCLUDE_PATH=/appl/python-2.7.14/include/python2.7
PWD=/project/voight_ML/thomc/thomc_results/VirtualFlow/VFLP/VFLP-trial/tools
_LMFILES_=/appl/Modules/modulefiles/gcc/4.9.4:/appl/Modules/CentOS7/python/2:/appl/Modules/modulefiles/openmpi/1.8.3:/appl/Modules/CentOS7/gsl/2.5:/appl/Modules/modulefiles/mpc/1.0.2
:/appl/Modules/modulefiles/mpfr/3.1.2:/appl/Modules/modulefiles/gmp/6.0.0:/appl/Modules/modulefiles/curl/7.37.0:/appl/Modules/modulefiles/liblapack/3.8.0:/appl/Modules/modulefiles/JA
GS/4.3.0:/appl/Modules/modulefiles/OpenBUGS/3.2.3:/appl/Modules/CentOS7/R/3.6.1:/appl/Modules/modulefiles/perl/5.20.2:/appl/Modules/CentOS7/python/3.6.5:/appl/Modules/modulefiles/gnu
plot/4.6.5:/appl/Modules/CentOS7/liftOver/20180423:/appl/Modules/modulefiles/mysql/5.6.17:/appl/Modules/modulefiles/emacs/24.3:/appl/Modules/modulefiles/bamtools/2.3.0:/appl/Modules/
modulefiles/annovar/2019Oct24:/appl/Modules/modulefiles/bedtools2/2.25.0:/appl/Modules/modulefiles/vcftools/0.1.12b:/appl/Modules/modulefiles/git/2.5.0:/appl/Modules/modulefiles/STAR
/2.5.1B:/appl/Modules/modulefiles/plink/1.07:/appl/Modules/CentOS7/vftools/1.0:/appl/Modules/CentOS7/qvina/2.0
CUDA_VISIBLE_DEVICES=
LSB_RES_GET_FANOUT_INFO=Y
LANG=en_US.UTF-8
LSB_CHKFILENAME=/home/thomc/.lsbatch/1601547443.6946271
MODULEPATH=/appl/Modules/CentOS7:/appl/Modules/versions:/appl/Modules/$MODULE_VERSION/modulefiles:/appl/Modules/modulefiles
CHAINPATH=/appl/liftOver-20180423/chains
LOADEDMODULES=gcc/4.9.4:python/2:openmpi/1.8.3:gsl/2.5:mpc/1.0.2:mpfr/3.1.2:gmp/6.0.0:curl/7.37.0:liblapack/3.8.0:JAGS/4.3.0:OpenBUGS/3.2.3:R/3.6.1:perl/5.20.2:python/3.6.5:gnuplot/4
.6.5:liftOver/20180423:mysql/5.6.17:emacs/24.3:bamtools/2.3.0:annovar/2019Oct24:bedtools2/2.25.0:vcftools/0.1.12b:git/2.5.0:STAR/2.5.1B:plink/1.07:vftools/1.0:qvina/2.0
LSB_DJOB_HOSTFILE=/home/thomc/.lsbatch/1601547443.6946271.hostfile
LAPACKE_LIBRARIES=/appl/lapack-3.8.0/lib64
LSF_JOB_TIMESTAMP_VALUE=1601547443
LSB_AFFINITY_HOSTFILE=/home/thomc/.lsbatch/1601547443.6946271.hostAffinityFile
options=BIOCINSTALLER_ONLINE_DCF=FALSE
LSB_DJOB_NUMPROC=1
LSB_EXEC_HOSTTYPE=X86_64
LSF_BINDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/bin
KRB5CCNAME=/tmp/lsf_krb5cc_j6946271_0
HISTCONTROL=ignoredups
SHLVL=6
HOME=/home/thomc
USER_MODULES=JAGS/4.3.0 OpenBUGS/3.2.3 R/3.6.1 perl/5.20.2 python/3.6.5 gnuplot/4.6.5 liftOver/20180423 mysql/5.6.17 emacs/24.3 curl/7.37.0 bamtools/2.3.0 annovar/2019Oct24 bedtools2
/2.25.0 vcftools/0.1.12b git/2.5.0 STAR/2.5.1B plink/1.07 vftools/1.0
JOB_TERMINATE_INTERVAL=10
LSB_ACCT_FILE=/tmp/6946271.tmpdir/.1601547443.6946271.acct
BINARY_TYPE_HPC=
controlfile=../../workflow/control/all.ctrl
LPC_MODULES=gcc/4.9.4 python/2 openmpi/1.8.3 gsl mpc mpfr gmp curl
LSB_SUB_HOST=inexorable
LSFUSER=thomc
__LSF_JOB_TMPDIR__=/tmp/6946271.tmpdir
LSB_SUB_USER=thomc
LOGNAME=thomc
LSB_MCPU_HOSTS=devastator 1 
LSB_OUTDIR=/project/voight_ML/thomc/thomc_results/VirtualFlow/VFLP/VFLP-trial/tools
LSB_OUTPUTFILE=../workflow/output-files/jobs/job-1.1_6946271.out
LSB_QUEUE=voight_normal
SSH_CONNECTION=72.78.190.137 52378 172.16.47.180 22
LSB_DEFAULTQUEUE=voight_normal
MODULESHOME=/appl/Modules/3.2.10
LSF_CGROUP_TOPDIR_KEY=PMACS-SCC
LESSOPEN=||/usr/bin/lesspipe.sh %s
LSB_XFER_OP=
LSB_EEXEC_REAL_GID=
LSF_ENVDIR=/lsf/conf
LSB_DJOB_RANKFILE=/home/thomc/.lsbatch/1601547443.6946271.hostfile
LSF_EGO_ENVDIR=/lsf/conf/ego/PMACS-SCC/kernel
G_BROKEN_FILENAMES=1
BASH_FUNC_module()=() {  eval `/appl/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/bin/env

Job infos by bjobs
------------------------
Job <6946271> is not found

                    *** Job Output ***                    
===========================================================

++ grep -m 1 '^tempdir=' ../workflow/control/all.ctrl
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ export VF_TMPDIR=/dev/shm
+ VF_TMPDIR=/dev/shm
+ '[' '!' -d /dev/shm/thomc ']'
++ grep -m 1 '^job_letter=' ../workflow/control/all.ctrl
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ VF_JOBLETTER=c
+ export VF_JOBLETTER
++ grep -m 1 '^error_sensitivity=' ../workflow/control/all.ctrl
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ VF_ERROR_SENSITIVITY=normal
+ export VF_ERROR_SENSITIVITY
+ [[ normal == \h\i\g\h ]]
++ grep -m 1 '^error_response=' ../workflow/control/all.ctrl
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ VF_ERROR_RESPONSE=fail
+ export VF_ERROR_RESPONSE
+ check_queue_end1
+ VF_CONTROLFILE=
++ ls '../workflow/control/*-*'
++ true
+ '[' -z '' ']'
+ export VF_CONTROLFILE=../workflow/control/all.ctrl
+ VF_CONTROLFILE=../workflow/control/all.ctrl
++ cat ../workflow/control/all.ctrl
++ grep stop_after_next_check_interval=
+ line=stop_after_next_check_interval=false
+ stop_after_next_check_interval=false
+ '[' false = true ']'
+ no_collections_incomplete=0
+ i=0
+ '[' 0 == 0 ']'
++ grep -c '[^[:blank:]]'
++ cat ../workflow/ligand-collections/todo/todo.all ../workflow/ligand-collections/todo/todo.all.0000 '../workflow/ligand-collections/todo/1/*/*' '../workflow/ligand-collections/curr
ent/1/*/*'
+ no_collections_incomplete=2
+ i=1
+ '[' 1 == 5 ']'
+ sleep 1
+ '[' 2 == 0 ']'
+ [[ 2 = \0 ]]
++ grep -m 1 -- '-W ' ../workflow/job-files/main/1.job
+ job_line='#BSUB -W 01:00'
+ timelimit=' 01:00'
++ echo -n ' 01:00'
++ awk -F : '{print $2 * 60 + $1 * 3600 }'
+ export VF_TIMELIMIT_SECONDS=3600
+ VF_TIMELIMIT_SECONDS=3600
++ cat ../workflow/control/all.ctrl
++ grep -m 1 queues_per_step=
+ line=queues_per_step=1
+ export VF_QUEUES_PER_STEP=1
+ VF_QUEUES_PER_STEP=1
++ grep -m 1 '^prepare_queue_todolists=' ../workflow/control/all.ctrl
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ prepare_queue_todolists=true
+ '[' TRUE == TRUE ']'
+ cd helpers
+ bash prepare-todolists.sh 1 1 1
+ echo -e '\n * Preparing the to-do lists for jobline 1\n'

 * Preparing the to-do lists for jobline 1

+ trap time_near_limit 10
+ trap termination_signal 1 2 3 9 15
+ trap clean_up EXIT
+ mkdir -p /dev/shm/thomc/VFLP/c/1/prepare-todolists/
+ vf_controlfile_temp=/dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
+ cp ../../workflow/control/all.ctrl /dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
++ grep -m 1 '^collection_folder=' /dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ collection_folder=../input-files/FA/
+ collection_folder=../input-files/FA
++ grep -m 1 '^ligands_todo_per_queue=' /dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ ligands_todo_per_queue=500000
++ grep -m 1 '^ligands_per_refilling_step=' /dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ ligands_per_refilling_step=10000
+ [[ ! 1 1 1 = *\q\u\i\e\t* ]]
+ echo

+ ligands_todo=
+ queue_collection_numbers=
+ todofile_queue_old_temp=/dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.queue.old
++ seq 1 1
+ for queue_no_2 in '$(seq 1 ${steps_per_job})'
++ seq 1 1
+ for queue_no_3 in '$(seq 1 ${queues_per_step})'
+ queue_no=1-1-1
+ ligands_todo[${queue_no_2}0000${queue_no_3}]=0
+ queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=0
+ todofile_queue_new_temp[${queue_no_2}0000${queue_no_3}]=/dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.queue.new.1-1-1
+ '[' -s ../../workflow/ligand-collections/todo/1/1/1-1-1 ']'
+ '[' -s ../../workflow/ligand-collections/current/1/1/1-1-1 ']'
+ [[ ! 1 1 1 = *\q\u\i\e\t* ]]
+ echo 'Starting the (re)filling of the todolists of the queues.'
Starting the (re)filling of the todolists of the queues.
+ echo

++ seq 1 1
+ for queue_no_2 in '$(seq 1 ${steps_per_job})'
++ seq 1 1
+ for queue_no_3 in '$(seq 1 ${queues_per_step})'
+ queue_no=1-1-1
+ echo 'Before (re)filling the todolists the queue 1-1-1 had 0 ligands todo distributed in 0 collections.'
Before (re)filling the todolists the queue 1-1-1 had 0 ligands todo distributed in 0 collections.
+ echo

+ status=false
+ k=1
+ max_iter=1000
+ modification_time_difference=0
++ date +%s
+ start_time_waiting=1601547446
++ grep -m 1 '^dispersion_time_min=' /dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ dispersion_time_min=3
++ grep -m 1 '^dispersion_time_max=' /dev/shm/thomc/VFLP/c/1/prepare-todolists/controlfile
++ tr -d '[[:space:]]'
++ awk -F '[=#]' '{print $2}'
+ dispersion_time_max=10
++ shuf -i 3-10 -n1
+ modification_time_treshhold=8
+ modification_time_treshhold_lockedfile=300
+ [[ false = \f\a\l\s\e ]]
++ stat -c %Z ../../workflow/ligand-collections/todo/todo.all
+ modification_time=1601547142
+ '[' 1601547142 -eq 1601547142 ']'
++ date +%s
+ modification_time_difference=304
+ '[' 304 -ge 8 ']'
+ mv ../../workflow/ligand-collections/todo/todo.all ../../workflow/ligand-collections/todo/todo.all.locked
+ cp ../../workflow/ligand-collections/todo/todo.all.locked /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
++ realpath ../../workflow/ligand-collections/todo/todo.all.locked
++ xargs basename
++ xargs basename
++ awk -F . '{print $3}'
+ current_todo_list_index=0000
+ '[' 0000 -eq 0000 ']'
+ cp /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all ../../workflow/ligand-collections/var/todo.all.0000.bak.1
+ status=true
+ trap 'error_response_std $LINENO' ERR
+ touch_locked_pid='#!'
+ [[ true = \f\a\l\s\e ]]
+ watch -m -n 1 touch ../../workflow/ligand-collections/var/todo.all.locked
++ date +%s
+ end_time_waiting=1601547446
++ cat /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
++ grep -c '[^[:blank:]]'
+ no_collections_incomplete=1
+ [[ 1 = \0 ]]
+ grep '[^[:blank:]]'
+ mv /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all.tmp /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ no_of_refilling_steps=50
++ grep -cv '^\s*$' /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ no_collections_remaining=1
+ no_collections_assigned=0
+ no_collections_beginning=1
++ date +%s
+ start_time_seconds=1601547446
++ seq 1 50
+ for refill_step in '$(seq 1 ${no_of_refilling_steps})'
+ step_limit=10000
++ seq 1 1
+ for queue_no_2 in '$(seq 1 ${steps_per_job})'
++ seq 1 1
+ for queue_no_3 in '$(seq 1 ${queues_per_step})'
+ queue_no=1-1-1
+ '[' 0 -lt 10000 ']'
+ '[' 1 -eq 0 ']'
++ head -n 1 /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ next_ligand_collection_and_length='FDAAPP_00000 2908'
+ next_ligand_collection=FDAAPP_00000
+ echo 'FDAAPP_00000 2908'
+ no_to_add=2908
+ '[' 2908 -eq 2908 ']'
+ ligands_todo[${queue_no_2}0000${queue_no_3}]=2908
+ queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
+ tail -n +2 /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ mv /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all.tmp /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ no_collections_remaining=0
+ no_collections_assigned=1
+ '[' 2908 -lt 10000 ']'
+ '[' 0 -eq 0 ']'
+ next_todo_list1
+ '[' 0000 -eq 0000 ']'
++ printf %04d 1
+ next_todo_list_index=0001
+ next_todo_list=../../workflow/ligand-collections/todo/todo.all.0001
+ '[' -f ../../workflow/ligand-collections/todo/todo.all.0001 ']'
++ printf %04d -1
+ next_todo_list_index=-001
+ next_todo_list=../../workflow/ligand-collections/todo/todo.all.-001
+ no_collections_remaining=0
+ echo ' * Info: No more todo lists.'
 * Info: No more todo lists.
+ [[ 0 = \0 ]]
+ next_todo_list2
+ [[ -f ../../workflow/ligand-collections/todo/todo.all.locked ]]
+ echo ' * Warning: There exists an old (locked) todo file. Trying to take care of it...'
 * Warning: There exists an old (locked) todo file. Trying to take care of it...
+ [[ ! -L ../../workflow/ligand-collections/todo/todo.all.locked ]]
+ echo ' * Warning: The old todo file is a symlink or an empty file. Removing it...'
 * Warning: The old todo file is a symlink or an empty file. Removing it...
+ rm ../../workflow/ligand-collections/todo/todo.all.locked
++ grep -v total
++ grep -v ' 0 '
++ wc -l ../../workflow/ligand-collections/todo/todo.all.0000
++ head -n 1
++ awk '{print $2}'
+ next_todo_list=../../workflow/ligand-collections/todo/todo.all.0000
+ next_todo_list_index=0000
+ '[' -n 0000 ']'
+ ln -s todo.all.0000 ../../workflow/ligand-collections/todo/todo.all.locked
+ echo 'The next todo list will be used (todo.all.0000)'
The next todo list will be used (todo.all.0000)
+ cp ../../workflow/ligand-collections/todo/todo.all.0000 /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ echo -n ''
+ '[' -f /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all.old ']'
+ current_todo_list_index=0000
+ current_todo_list=../../workflow/ligand-collections/todo/todo.all.0000
++ grep -cv '^\s*$' /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ no_collections_remaining=1
+ no_collections_assigned=0
+ no_collections_beginning=1
+ [[ 1 = \0 ]]
++ head -n 1 /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ next_ligand_collection_and_length='FDAAPP_00000 2908'
+ next_ligand_collection=FDAAPP_00000
+ echo 'FDAAPP_00000 2908'
+ no_to_add=2908
+ '[' 2908 -eq 2908 ']'
+ ligands_todo[${queue_no_2}0000${queue_no_3}]=5816
+ queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=2
+ tail -n +2 /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ mv /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all.tmp /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ no_collections_remaining=0
+ no_collections_assigned=1
+ '[' 5816 -lt 10000 ']'
+ '[' 0 -eq 0 ']'
+ next_todo_list1
+ '[' 0000 -eq 0000 ']'
++ printf %04d 1
+ next_todo_list_index=0001
+ next_todo_list=../../workflow/ligand-collections/todo/todo.all.0001
+ '[' -f ../../workflow/ligand-collections/todo/todo.all.0001 ']'
++ printf %04d -1
+ next_todo_list_index=-001
+ next_todo_list=../../workflow/ligand-collections/todo/todo.all.-001
+ no_collections_remaining=0
+ echo ' * Info: No more todo lists.'
 * Info: No more todo lists.
+ [[ 0 = \0 ]]
+ next_todo_list2
+ [[ -f ../../workflow/ligand-collections/todo/todo.all.locked ]]
+ echo ' * Warning: There exists an old (locked) todo file. Trying to take care of it...'
 * Warning: There exists an old (locked) todo file. Trying to take care of it...
+ [[ ! -L ../../workflow/ligand-collections/todo/todo.all.locked ]]
+ echo ' * Warning: The old todo file is a symlink or an empty file. Removing it...'
 * Warning: The old todo file is a symlink or an empty file. Removing it...
+ rm ../../workflow/ligand-collections/todo/todo.all.locked
++ grep -v total
++ grep -v ' 0 '
++ head -n 1
++ wc -l ../../workflow/ligand-collections/todo/todo.all.0000
++ awk '{print $2}'
+ next_todo_list=../../workflow/ligand-collections/todo/todo.all.0000
+ next_todo_list_index=0000
+ '[' -n 0000 ']'
+ ln -s todo.all.0000 ../../workflow/ligand-collections/todo/todo.all.locked
+ echo 'The next todo list will be used (todo.all.0000)'
The next todo list will be used (todo.all.0000)
+ cp ../../workflow/ligand-collections/todo/todo.all.0000 /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
+ echo -n ''
+ '[' -f /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all.old ']'
+ current_todo_list_index=0000
+ current_todo_list=../../workflow/ligand-collections/todo/todo.all.0000
++ grep -cv '^\s*$' /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all
++ true
+ no_collections_remaining=0
+ no_collections_assigned=0
+ no_collections_beginning=0
+ [[ 0 = \0 ]]
+ echo 'There is no more ligand collection in the todo.all file. Stopping the refilling procedure.'
There is no more ligand collection in the todo.all file. Stopping the refilling procedure.
+ break 4
++ seq 1 1
+ for queue_no_2 in '$(seq 1 ${steps_per_job})'
++ seq 1 1
+ for queue_no_3 in '$(seq 1 ${queues_per_step})'
+ queue_no=1-1-1
+ mkdir -p ../../workflow/ligand-collections/todo/1/1/
+ '[' -f /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.queue.new.1-1-1 ']'
+ cat /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.queue.new.1-1-1
+ rm /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.queue.new.1-1-1
+ [[ ! 1 1 1 = *\q\u\i\e\t* ]]
++ seq 1 1
+ for queue_no_2 in '$(seq 1 ${steps_per_job})'
++ seq 1 1
+ for queue_no_3 in '$(seq 1 ${queues_per_step})'
+ queue_no=1-1-1
+ echo 'After (re)filling the todolists the queue 1-1-1 has 5816 ligands todo distributed in 2 collections.'
After (re)filling the todolists the queue 1-1-1 has 5816 ligands todo distributed in 2 collections.
+ [[ ! 1 1 1 = *\q\u\i\e\t* ]]
++ date +%s
+ end_time_seconds=1601547446
+ echo

+ echo 'The todo lists for the queues were (re)filled in 0 second(s) (waiting time not included).'
The todo lists for the queues were (re)filled in 0 second(s) (waiting time not included).
+ echo 'The waiting time was 0 second(s).'
The waiting time was 0 second(s).
+ echo

+ clean_up
+ cp /dev/shm/thomc/VFLP/c/1/prepare-todolists/todo.all ../../workflow/ligand-collections/todo/todo.all.locked
+ mv ../../workflow/ligand-collections/todo/todo.all.locked ../../workflow/ligand-collections/todo/todo.all
+ rm -r /dev/shm/thomc/VFLP/c/1/prepare-todolists/
+ kill '#!'
+ true
+ cd ..
++ seq 1 1
+ for VF_STEP_NO in '$(seq 1 ${VF_NODES_PER_JOB} )'
+ export VF_STEP_NO
++ hostname
+ echo 'Starting job step VF_STEP_NO on host devastator.'
Starting job step VF_STEP_NO on host devastator.
+ sleep 1
+ bash ../workflow/job-files/sub/one-step.sh
Error was trapped
Error in bash script one-step.sh
Error on line 214
Environment variables
----------------------------------
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VF_OLD_JOB_NO=1.1
VF_JOBLETTER=c
MANPATH=/appl/git-2.5.0/share/man:/appl/vcftools-0.1.12b/man:/appl/emacs-24.3/share/man:/appl/mysql-5.6.17/man:/appl/gnuplot-4.6.5/share/man:/appl/python-3.6.5/man:/appl/perl-5.20.2/
man:/appl/R-3.6.1/man:/appl/OpenBUGS-3.2.3/share/man:/appl/JAGS-4.3.0/man:/appl/lapack-3.8.0/man:/appl/curl-7.37.0/share/man:/appl/gsl-2.5/share/man:/appl/openmpi-1.8.3/share/man:/ap
pl/python-2.7.14/man:/appl/gcc-4.9.4/man:/lsf/10.1/man:
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VF_STARTINGTIME=Thu Oct  1 06:17:25 EDT 2020
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SHELL=/bin/bash
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SSH_CLIENT=72.78.190.137 52378 22
LSB_TRAPSIGS=trap # 15 10 12 2 1
LS_EXECCWD=/project/voight_ML/thomc/thomc_results/VirtualFlow/VFLP/VFLP-trial/tools
PERL5LIB=/appl/vcftools-0.1.12b/perl:/appl/perl-5.20.2/lib/5.20.2
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VF_CONTROLFILE=../workflow/control/all.ctrl
LSB_JOB_EXECUSER=thomc
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VF_VF_OLD_JOB_NO_2=1
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LC_ALL=C
LSF_LIBDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/lib
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eg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.
rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.ax
v=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.r
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LD_LIBRARY_PATH=/lsf/10.1/linux3.10-glibc2.17-x86_64/lib:/appl/git-2.5.0/lib:/appl/vcftools-0.1.12b/lib:/appl/bamtools-2.3.0/lib:/appl/mysql-5.6.17/lib:/appl/python-3.6.5/lib:/appl/p
erl-5.20.2/lib:/appl/R-3.6.1/lib:/appl/R-3.6.1/lib64/R/lib:/appl/OpenBUGS-3.2.3/lib:/appl/JAGS-4.3.0/lib64:/appl/lapack-3.8.0/lib64:/appl/curl-7.37.0/lib:/appl/gmp-6.0.0/lib:/appl/mp
fr-3.1.2/lib:/appl/mpc-1.0.2/lib:/appl/gsl-2.5/lib:/appl/openmpi-1.8.3/lib:/appl/python-2.7.14/lib:/appl/gcc-4.9.4/lib64:/appl/gcc-4.9.4/lib:/lsf/10.1/linux2.6-glibc2.3-x86_64/lib
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CPATH=/appl/bamtools-2.3.0/include:/appl/python-3.6.5/include:/appl/JAGS-4.3.0/include:/appl/gmp-6.0.0/include:/appl/mpfr-3.1.2/include:/appl/mpc-1.0.2/include:/appl/gsl-2.5/include/
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CHAINPATH=/appl/liftOver-20180423/chains
LAPACKE_LIBRARIES=/appl/lapack-3.8.0/lib64
LSF_JOB_TIMESTAMP_VALUE=1601547443
LSB_AFFINITY_HOSTFILE=/home/thomc/.lsbatch/1601547443.6946271.hostAffinityFile
LSF_BINDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/bin
LSB_EXEC_HOSTTYPE=X86_64
LSB_DJOB_NUMPROC=1
options=BIOCINSTALLER_ONLINE_DCF=FALSE
HISTCONTROL=ignoredups
KRB5CCNAME=/tmp/lsf_krb5cc_j6946271_0
VF_TMPDIR=/dev/shm
VF_JOBLINE_NO=1
HOME=/home/thomc
SHLVL=7
enl=
JOB_TERMINATE_INTERVAL=10
USER_MODULES=JAGS/4.3.0 OpenBUGS/3.2.3 R/3.6.1 perl/5.20.2 python/3.6.5 gnuplot/4.6.5 liftOver/20180423 mysql/5.6.17 emacs/24.3 curl/7.37.0 bamtools/2.3.0 annovar/2019Oct24 bedtools2
/2.25.0 vcftools/0.1.12b git/2.5.0 STAR/2.5.1B plink/1.07 vftools/1.0
BINARY_TYPE_HPC=
LSB_ACCT_FILE=/tmp/6946271.tmpdir/.1601547443.6946271.acct
LSB_SUB_HOST=inexorable
LPC_MODULES=gcc/4.9.4 python/2 openmpi/1.8.3 gsl mpc mpfr gmp curl
controlfile=../../workflow/control/all.ctrl
LSB_SUB_USER=thomc
__LSF_JOB_TMPDIR__=/tmp/6946271.tmpdir
LSFUSER=thomc
VF_NODES_PER_JOB=1
LSB_QUEUE=voight_normal
LSB_OUTPUTFILE=../workflow/output-files/jobs/job-1.1_6946271.out
LSB_OUTDIR=/project/voight_ML/thomc/thomc_results/VirtualFlow/VFLP/VFLP-trial/tools
LSB_MCPU_HOSTS=devastator 1 
LOGNAME=thomc
VF_TIMELIMIT_SECONDS=3600
SSH_CONNECTION=72.78.190.137 52378 172.16.47.180 22
MODULESHOME=/appl/Modules/3.2.10
LSB_DEFAULTQUEUE=voight_normal
LESSOPEN=||/usr/bin/lesspipe.sh %s
LSF_CGROUP_TOPDIR_KEY=PMACS-SCC
LSB_XFER_OP=
LSB_EEXEC_REAL_GID=
VF_BATCHSYSTEM=LSF
LSF_ENVDIR=/lsf/conf
VF_QUEUES_PER_STEP=1
G_BROKEN_FILENAMES=1
LSF_EGO_ENVDIR=/lsf/conf/ego/PMACS-SCC/kernel
LSB_DJOB_RANKFILE=/home/thomc/.lsbatch/1601547443.6946271.hostfile
VF_ERROR_SENSITIVITY=normal
BASH_FUNC_module()=() {  eval `/appl/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
_=/usr/bin/env

 * Trying to stop this queue and causing the jobline to fail...
cp: cannot stat '/dev/shm/thomc/VFLP/c//-1/workflow/output-files/queues/1//queue--1.*': No such file or directory
+ wait
+ echo

+ echo

+ echo '                  *** Preparing the next batch system job ***                     '
                  *** Preparing the next batch system job ***                     
+ echo ==================================================================================
==================================================================================
+ echo

+ check_queue_end2
+ check_queue_end1
+ VF_CONTROLFILE=
++ ls '../workflow/control/*-*'
++ true
+ '[' -z '' ']'
+ export VF_CONTROLFILE=../workflow/control/all.ctrl
+ VF_CONTROLFILE=../workflow/control/all.ctrl
++ cat ../workflow/control/all.ctrl
++ grep stop_after_next_check_interval=
+ line=stop_after_next_check_interval=false
+ stop_after_next_check_interval=false
+ '[' false = true ']'
+ no_collections_incomplete=0
+ i=0
+ '[' 0 == 0 ']'
++ grep -c '[^[:blank:]]'
++ cat ../workflow/ligand-collections/todo/todo.all ../workflow/ligand-collections/todo/todo.all.0000 ../workflow/ligand-collections/todo/1/1/1-1-1 '../workflow/ligand-collections/cu
rrent/1/*/*'
+ no_collections_incomplete=2
+ i=1
+ '[' 1 == 5 ']'
+ sleep 1
+ '[' 2 == 0 ']'
+ [[ 2 = \0 ]]
++ cat ../workflow/control/all.ctrl
++ grep stop_after_job=
+ line=stop_after_job=false
+ stop_after_job=false
+ '[' false = true ']'
+ cd helpers
+ . sync-jobfile.sh 1
++ '[' 1 = -h ']'
++ [[ 1 -ne 1 ]]
++ trap 'error_response_nonstd $LINENO' ERR
++ jobline_no=1
++ controlfile=
+++ ls '../../workflow/control/*-*'
+++ true
++ '[' -z '' ']'
++ export controlfile=../../workflow/control/all.ctrl
++ controlfile=../../workflow/control/all.ctrl
+++ grep -m 1 '^batchsystem=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ batchsystem=LSF
++ echo -e 'Syncing the jobfile of jobline 1 with the controlfile file ../../workflow/control/all.ctrl.'
Syncing the jobfile of jobline 1 with the controlfile file ../../workflow/control/all.ctrl.
+++ grep -m 1 '^steps_per_job=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ steps_per_job_new=1
++ '[' LSF = SLURM ']'
++ [[ LSF = \T\O\R\Q\U\E ]]
++ [[ LSF = \P\B\S ]]
+++ grep -m 1 '^cpus_per_step=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ cpus_per_step_new=1
++ '[' LSF = SLURM ']'
++ [[ LSF = \T\O\R\Q\U\E ]]
++ [[ LSF = \P\B\S ]]
++ '[' LSF = LSF ']'
+++ grep -m 1 '\-n' ../../workflow/job-files/main/1.job
++ job_line='#BSUB -n 1'
++ cpus_per_step_old=1
++ sed -i 's/-n 1/-n 1/g' ../../workflow/job-files/main/1.job
++ sed -i s/ptile=1/ptile=1/g ../../workflow/job-files/main/1.job
+++ cat ../../workflow/control/all.ctrl
+++ grep -m 1 '^timelimit='
++ line=timelimit=01:00
+++ grep -m 1 '^timelimit=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ timelimit_new=01:00
++ '[' LSF == SLURM ']'
++ [[ LSF = \T\O\R\Q\U\E ]]
++ [[ LSF = \P\B\S ]]
++ '[' LSF == SGE ']'
++ '[' LSF == LSF ']'
+++ grep -m 1 '^#BSUB \-W ' ../../workflow/job-files/main/1.job
++ job_line='#BSUB -W 01:00'
++ timelimit_old=01:00
++ sed -i s/01:00/01:00/g ../../workflow/job-files/main/1.job
+++ cat ../../workflow/control/all.ctrl
+++ grep -m 1 '^partition='
++ line=partition=voight_normal
+++ grep -m 1 '^partition=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ partition_new=voight_normal
++ '[' LSF = SLURM ']'
++ [[ LSF = \T\O\R\Q\U\E ]]
++ [[ LSF = \P\B\S ]]
++ '[' LSF = SGE ']'
++ '[' LSF = LSF ']'
++ sed -i 's/^#BSUB -q .*/#BSUB -q voight_normal/g' ../../workflow/job-files/main/1.job
+++ cat ../../workflow/control/all.ctrl
+++ grep -m 1 '^job_letter='
++ line=job_letter=c
+++ grep -m 1 '^job_letter=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ job_letter_new=c
++ '[' LSF = SLURM ']'
++ [[ LSF = \T\O\R\Q\U\E ]]
++ [[ LSF = \P\B\S ]]
++ '[' LSF = SGE ']'
++ '[' LSF = LSF ']'
++ sed -i 's/^#BSUB -J [a-zA-Z]/#BSUB -J c/g' ../../workflow/job-files/main/1.job
+ cd ..
+ new_job_no_2=2
+ new_job_no=1.2
+ sed -i 's/^#BSUB -J c-.*/#BSUB -J c-1.2/g' ../workflow/job-files/main/1.job
+ sed -i 's|^#BSUB -oo ../workflow/output-files/jobs/job-1.1_%J.out|#BSUB -oo ../workflow/output-files/jobs/job-1.2_%J.out|g' ../workflow/job-files/main/1.job
++ date +%s
+ end_time_seconds=1601547449
+ time_diff=4
+ treshhold=100
+ '[' 4 -le 100 ']'
+ echo 'Since the beginning of the job less than 100 seconds have passed.'
Since the beginning of the job less than 100 seconds have passed.
+ echo 'Sleeping for some while to prevent a job submission run...'
Sleeping for some while to prevent a job submission run...
+ sleep 120
+ cd helpers
+ . submit.sh ../workflow/job-files/main/1.job
++ usage='# Usage: . submit jobfile [quiet]'
++ '[' ../workflow/job-files/main/1.job == -h ']'
++ [[ 1 -ne 1 ]]
++ trap 'error_response_nonstd $LINENO' ERR
+++ grep -m 1 '^batchsystem=' ../../workflow/control/all.ctrl
+++ tr -d '[[:space:]]'
+++ awk -F '[=#]' '{print $2}'
++ batchsystem=LSF
++ jobfile=../workflow/job-files/main/1.job
+++ echo ../workflow/job-files/main/1.job
+++ awk -F '[./]' '{print $(NF-1)}'
++ jobline=1
++ cd ../
++ '[' LSF == SLURM ']'
++ [[ LSF = \T\O\R\Q\U\E ]]
++ [[ LSF = \P\B\S ]]
++ '[' LSF == SGE ']'
++ '[' LSF == LSF ']'
++ bsub
Job <6946272> is submitted to queue <voight_normal>.
++ cd helpers
++ '[' '!' ../workflow/job-files/main/1.job = '*quiet*' ']'
+++ date
++ echo 'The job for jobline 1 has been submitted at Thu Oct  1 06:19:29 EDT 2020.'
The job for jobline 1 has been submitted at Thu Oct  1 06:19:29 EDT 2020.
++ echo

+ cd ..
+ print_job_infos_end
+ echo

+ echo '                     *** Final Job Information ***                    '
                     *** Final Job Information ***                    
+ echo ======================================================================
======================================================================
+ echo

+ echo 'Starting time:' Thu Oct 1 06:17:25 EDT 2020
Starting time: Thu Oct 1 06:17:25 EDT 2020
++ date
+ echo 'Ending time:  ' Thu Oct 1 06:19:29 EDT 2020
Ending time:   Thu Oct 1 06:19:29 EDT 2020
+ echo