+ input_assembly_merged_fasta=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-polish_merge/execution/assembly.merged.fasta
+ input_p_ctg_fasta=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/p_ctg.fasta
+ input_a_ctg_fasta=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/a_ctg.fasta
+ params_log_level=INFO
+ params_tmp_dir=/tmp
+ params_polish_run=1
+ output_p_ctg_fasta=p_ctg.fasta
+ output_a_ctg_fasta=a_ctg.fasta
+ ipa2-task separate_p_from_a
 ;;
 ;;
 ;;
}
}
}
BASH_ENV=/usr/share/lmod/lmod/init/bash
BASH_FUNC_ml%%=() {  eval "$($LMOD_DIR/ml_cmd "$@")"
BASH_FUNC_module%%=() {  if [ -z "${LMOD_SH_DBG_ON+x}" ]; then
BASH_FUNC_which%%=() {  unset -f which;
BINARY_TYPE_HPC=
BSUB_BLOCK_EXEC_HOST=
 case "$-" in 
CROMWELL_CONFIG_FILE=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell.conf
CROMWELL_JAVA_HOME=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/java/cromwell/cromwell_74/binwrap/../../../../../thirdparty/java/jre/jre_11.0.12+7
CROMWELL_JAVA_OPTS=-Djava.library.path=
CROMWELL_PATH=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/java/cromwell/cromwell_69-pacbio1/binwrap:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../../private/otherbins/runtime/bin:/usr/bin:/bin:/usr/bin:/bin
CUDA_VISIBLE_DEVICES=
CUDA_VISIBLE_DEVICES_ORIG=
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/10025/bus
 echo "Shell debugging restarted" 1>&2;
 echo "Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output" 1>&2;
 esac;
 eval "$($LMOD_CMD shell "$@")" && eval "$(${LMOD_SETTARG_CMD:-:} -s sh)";
 fi;
 fi;
 fi;
FPATH=/usr/share/lmod/lmod/init/ksh_funcs
GPU_DEVICE_ORDINAL=
HIP_VISIBLE_DEVICES=
HISTCONTROL=ignoredups
HISTSIZE=1000
HOME=/home/ellen.kittler-umw
HOSTNAME=r640c19
HOSTTYPE=X86_64
IBM_JAVA_OPTIONS=-Xgcthreads4
 if [ -n "${__lmod_sh_dbg:-}" ]; then
 if [ -n "${__lmod_sh_dbg:-}" ]; then
input_a_ctg_fasta=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/a_ctg.fasta
input_assembly_merged_fasta=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-polish_merge/execution/assembly.merged.fasta
input_p_ctg_fasta=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/p_ctg.fasta
_JAVA_OPTIONS=-Djava.io.tmpdir=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/tmp.11d2d012
JAVA_OPTIONS=-XX:ParallelGCThreads=4
JOB_TERMINATE_INTERVAL=10
LANG=en_US.UTF-8
LANGUAGE=en_US:en:C
LC_ALL=en_US.UTF-8
LD_LIBRARY_PATH=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/gcc/gcc_10.3.0-2.17/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/libpng/libpng_1.6.37/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/libjpeg-turbo/libjpeg-turbo_2.1.0/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/freetype/freetype_2.11.0/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/htslib/htslib_1.17/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/openblas/openblas_0.3.17/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/zlib/zlib_1.2.11/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/bzip2/bzip2_1.0.8/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/xz/xz_5.2.5/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/ncurses/ncurses_6.2/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/readline/readline_8.1/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/openssl/openssl_1.1.1k/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/libffi/libffi_3.4.2/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/qhull/qhull_8.0.2/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/sqlite/sqlite_3.36.0/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/python/python3_3.9.6/lib:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/curl/curl_7.78.0/lib
LESSOPEN=||/usr/bin/lesspipe.sh %s
_LMFILES_=/share/modules/default/Core/smrtlink/13.1.0-sequel2.lua
LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod
LMOD_DIR=/usr/share/lmod/lmod/libexec
 __lmod_my_status=$?;
LMOD_PKG=/usr/share/lmod/lmod
__LMOD_REF_COUNT_MODULEPATH=/share/modules/default/Core:1;/etc/modulefiles:1;/usr/share/modulefiles:1;/usr/share/modulefiles/Linux:1;/usr/share/modulefiles/Core:1;/usr/share/lmod/lmod/modulefiles/Core:1
__LMOD_REF_COUNT_PATH=/share/pkg/smrtlink/13.1.0-sequel2/smrtcmds/bin:1;/share/pkg/singularity/3.10.2/bin:1;/lsf/10.1/linux3.10-glibc2.17-x86_64/bin:1;/home/ellen.kittler-umw/.local/bin:1;/home/ellen.kittler-umw/bin:1;/share/pkg/singularity/3.11.0/bin:1;/lsf/10.1/linux3.10-glibc2.17-x86_64/etc:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/opt/dell/srvadmin/bin:1;/opt/TurboVNC/bin:1
LMOD_ROOT=/usr/share/lmod
LMOD_SETTARG_FULL_SUPPORT=no
 __lmod_sh_dbg='v'
 __lmod_sh_dbg='vx'
 __lmod_sh_dbg='x'
LMOD_SITE_MODULEPATH=/share/modules/default/Core
LMOD_sys=Linux
LMOD_VERSION=8.7.53
LOADEDMODULES=smrtlink/13.1.0-sequel2
LOGNAME=ellen.kittler-umw
LSB_ACCT_FILE=/tmp/574087.tmpdir/.1751555876.574087.acct
LSB_AFFINITY_HOSTFILE=/home/ellen.kittler-umw/.lsbatch/1751555876.574087.hostAffinityFile
LSB_BATCH_JID=574087
LSB_BIND_CPU_LIST=1,3,5,7,8,9,11,12,13,15,17,19,21,23,25,27,28,29,31,32,33,35,36,37,39
LSB_CG_MEMLIMIT=0x138800000
LSB_CHKFILENAME=/home/ellen.kittler-umw/.lsbatch/1751555876.574087
LSB_DJOB_HOSTFILE=/home/ellen.kittler-umw/.lsbatch/1751555876.574087.hostfile
LSB_DJOB_NUMPROC=25
LSB_DJOB_RANKFILE=/home/ellen.kittler-umw/.lsbatch/1751555876.574087.hostfile
LSB_DOCKER_JOB_STARTTS=1751555877
LSB_ECHKPNT_RSH_CMD=/bin/ssh -i /root/.ssh/lsf_id_ed25519 -o 'PasswordAuthentication no'
LSB_EEXEC_REAL_GID=
LSB_EEXEC_REAL_UID=
LSB_EFFECTIVE_RSRCREQ=select[type == local] order[r15s:pg] rusage[mem=5000.00] span[hosts=1] affinity[core(1)*1:distribute=pack] 
LSB_EXEC_CLUSTER=sci
LSB_EXEC_HOSTTYPE=X86_64
LSB_EXIT_PRE_ABORT=99
LSB_HOSTS=r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19 r640c19
LSB_JOB_CGROUP_PARENT=/lsf/sci/job.574087.732689.1751555877
LSB_JOB_EXECUSER=ellen.kittler-umw
LSB_JOBEXIT_STAT=0
LSB_JOBFILENAME=/home/ellen.kittler-umw/.lsbatch/1751555876.574087
LSB_JOBID=574087
LSB_JOBINDEX=0
LSB_JOBNAME=/home/ellen.kittler-umw/scratch/mybinsh2/PacBio_DNassembly13.2v.sh final.consensusreadset.xml
LSB_JOB_NICE=0
LSB_JOBRES_CALLBACK=38455@r640c19
LSB_JOBRES_PID=732689
LSB_JOB_STARTER=source /lsf/conf/GLOBAL_JOB_ENVIRONMENT ; bash -c '%USRCMD'
LSB_MAX_NUM_PROCESSORS=25
LSB_MCPU_HOSTS=r640c19 25 
LSB_OUTDIR=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution
LSB_OUTPUTFILE=/home/ellen.kittler-umw/scratch/logs
LSB_PROJECT_NAME=default
LSB_QUEUE=long
LSB_RES_GET_FANOUT_INFO=Y
LSB_SUB_HOST=hpcc03
LSB_SUB_RES_REQ=rusage[mem=5000] span[hosts=1] 
LSB_SUB_USER=ellen.kittler-umw
LSB_TRAPSIGS=trap # 15 10 12 2 1
LSB_UNIXGROUP_INT=ellen.kittler-umw
LSB_XFER_OP=
LS_COLORS=rs=0:di=38;5;33:ln=38;5;51:mh=00: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=01;05;37;41: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;40:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=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:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.zst=38;5;9:*.tzst=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:*.wim=38;5;9:*.swm=38;5;9:*.dwm=38;5;9:*.esd=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.mjpg=38;5;13:*.mjpeg=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:*.mpeg=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:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.m4a=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:*.ra=38;5;45:*.wav=38;5;45:*.oga=38;5;45:*.opus=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
LS_EXECCWD=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution
LS_EXEC_T=START
LSF_BINDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/bin
LSF_CGROUP_TOPDIR_KEY=sci
LSF_ENVDIR=/lsf/conf
LSF_INVOKE_CMD=bsub
LSF_JOB_TIMESTAMP_VALUE=1751555877
__LSF_JOB_TMPDIR__=/tmp/574087.tmpdir
LSF_LIBDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/lib
LSF_LIM_API_NTRIES=1
LSF_LOGDIR=/lsf/log
LSF_SERVERDIR=/lsf/10.1/linux3.10-glibc2.17-x86_64/etc
LSFUSER=ellen.kittler-umw
LSF_VERSION=38
LS_JOBPID=732689
LS_SUBCWD=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution
MAIL=/var/spool/mail/ellen.kittler-umw
MANPATH=/usr/share/lmod/lmod/share/man:/lsf/10.1/man:
MODULEPATH_ROOT=/usr/share/modulefiles
MODULEPATH=/share/modules/default/Core:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
MODULESHOME=/usr/share/lmod/lmod
_ModuleTable001_=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
_ModuleTable002_=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
_ModuleTable_Sz_=2
MPLCONFIGDIR=/home/ellen.kittler-umw/.smrtlink/matplotlib
OLDPWD=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution
output_a_ctg_fasta=a_ctg.fasta
output_p_ctg_fasta=p_ctg.fasta
params_log_level=INFO
params_polish_run=1
params_tmp_dir=/tmp
PATH=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/pacbio/ipa2/binwrap/../../../../private/thirdparty/perl/perl_5.34.0/binwrap:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../thirdparty/java/cromwell/cromwell_69-pacbio1/binwrap:/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../../private/otherbins/runtime/bin:/usr/bin:/bin:/usr/bin:/bin
PWD=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution
PYTHONDONTWRITEBYTECODE=1
PYTHONNOUSERSITE=1
PYTHONPATH=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../site-packages
 return $__lmod_my_status
RM_CPUTASK10=17
RM_CPUTASK11=21
RM_CPUTASK12=25
RM_CPUTASK13=29
RM_CPUTASK14=33
RM_CPUTASK15=37
RM_CPUTASK16=3
RM_CPUTASK17=7
RM_CPUTASK1=8
RM_CPUTASK18=11
RM_CPUTASK19=15
RM_CPUTASK20=19
RM_CPUTASK2=12
RM_CPUTASK21=23
RM_CPUTASK22=27
RM_CPUTASK23=31
RM_CPUTASK24=35
RM_CPUTASK25=39
RM_CPUTASK3=28
RM_CPUTASK4=32
RM_CPUTASK5=36
RM_CPUTASK6=1
RM_CPUTASK7=5
RM_CPUTASK8=9
RM_CPUTASK9=13
ROCR_VISIBLE_DEVICES=
SBD_KRB5CCNAME_VAL=
 set +$__lmod_sh_dbg;
 set -$__lmod_sh_dbg;
SHELL=/bin/bash
SHLVL=10
SMRT_CHEMISTRY_BUNDLE_DIR=
SMRT_CROMWELL_ENV=true
__SMRTINTERNAL_ORIG__LD_LIBRARY_PATH=/lsf/10.1/linux3.10-glibc2.17-x86_64/lib
__SMRTINTERNAL_ORIG__PATH=
__SMRTINTERNAL_ORIG__PYTHONPATH=
SMRT_PIPELINE_BUNDLE_DIR=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/thirdparty/python3/python3_3.9.6/binwrap/../../../../pacbio/pbpipeline-resources
__SMRTPRIVATE_EXEPATH__perl=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/pacbio/ipa2/binwrap/../../../../private/thirdparty/perl/perl_5.34.0/binwrap/perl
SMRT_PYTHON3_PATH=/share/pkg/smrtlink/13.1.0-sequel2/install/smrtlink-release_13.1.0.221970/bundles/smrttools/install/smrttools-release_13.1.0.221970/private/pacbio/ipa2/binwrap/../../../../private/thirdparty/perl/perl_5.34.0/binwrap
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
SSH_CLIENT=146.189.92.95 39384 22
SSH_CONNECTION=146.189.92.95 39384 146.189.26.15 22
SSH_TTY=/dev/pts/34
TMPDIR=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/tmp.11d2d012
 unset __lmod_sh_dbg;
USER=ellen.kittler-umw
_=/usr/bin/env
 *v*)
 *v*x*)
 which "$1"
which_declare=declare -f
 *x*)
XDG_DATA_DIRS=/home/ellen.kittler-umw/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
XDG_RUNTIME_DIR=/run/user/10025
XDG_SESSION_ID=972788
XMODIFIERS=@im=ibus
+ [[ 1 -ge 1 ]]
+ echo 'IPA: Separate primary contigs from haplotigs for /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-polish_merge/execution/assembly.merged.fasta p_ctg.fasta a_ctg.fasta'
+ ln -sf /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/p_ctg.fasta in.p.fasta
+ ln -sf /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/inputs/250313208/a_ctg.fasta in.a.fasta
+ touch in.p.fasta.fai
+ [[ -s in.p.fasta ]]
+ IPA_TIME log.separate_p_from_a.samtools_faidx_p.memtime samtools faidx in.p.fasta
+ local local_out_memtime=log.separate_p_from_a.samtools_faidx_p.memtime
+ shift
+ local 'fmt_str=cmd: %C\nreal_time: %e s\nuser_time: %U s\nsys_time: %S s\nmax_rss: %M kB\nexit_status: %x'
+ local use_gnu_time=0
+ [[ -x /usr/bin/time ]]
+ /usr/bin/time '--format=cmd: %C\nreal_time: %e s\nuser_time: %U s\nsys_time: %S s\nmax_rss: %M kB\nexit_status: %x' -o /dev/null true
+ use_gnu_time=1
+ [[ 1 -eq 1 ]]
+ /usr/bin/time '--format=cmd: %C\nreal_time: %e s\nuser_time: %U s\nsys_time: %S s\nmax_rss: %M kB\nexit_status: %x' -o log.separate_p_from_a.samtools_faidx_p.memtime samtools faidx in.p.fasta
+ touch in.a.fasta.fai
+ [[ -s in.a.fasta ]]
+ IPA_TIME log.separate_p_from_a.samtools_faidx_a.memtime samtools faidx in.a.fasta
+ local local_out_memtime=log.separate_p_from_a.samtools_faidx_a.memtime
+ shift
+ local 'fmt_str=cmd: %C\nreal_time: %e s\nuser_time: %U s\nsys_time: %S s\nmax_rss: %M kB\nexit_status: %x'
+ local use_gnu_time=0
+ [[ -x /usr/bin/time ]]
+ /usr/bin/time '--format=cmd: %C\nreal_time: %e s\nuser_time: %U s\nsys_time: %S s\nmax_rss: %M kB\nexit_status: %x' -o /dev/null true
+ use_gnu_time=1
+ [[ 1 -eq 1 ]]
+ /usr/bin/time '--format=cmd: %C\nreal_time: %e s\nuser_time: %U s\nsys_time: %S s\nmax_rss: %M kB\nexit_status: %x' -o log.separate_p_from_a.samtools_faidx_a.memtime samtools faidx in.a.fasta
+ IPA_TIME log.separate_p_from_a.falconc.memtime falconc ipa-separate-p-from-a-with-fai --in_merged_fn=/home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-polish_merge/execution/assembly.merged.fasta --out-p=p_ctg.fasta --out-a=a_ctg.fasta --in-p-fai-fn in.p.fasta.fai --in-a-fai-fn in.a.fasta.fai
+ tee log.separate_p_from_a.falconc.tee
++ pwd
+ echo /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/p_ctg.fasta
++ pwd
+ echo /home/ellen.kittler-umw/Sequel2_PacBio/r54328U_20250625_165337/1_A01/ccs_consensus-11/cromwell-executions/pb_ccs/f4452ec2-59d1-4ba5-8a45-6d9228eb49ff/call-consolidate_reads_bam/execution/cromwell_out/cromwell-executions/pb_assembly_hifi/72f6f9f6-fbef-4386-9550-bafcc33dccd8/call-separate_p_from_a/execution/a_ctg.fasta