Martian Runtime - '3.1.0-v3.2.3'
2019-12-23 12:31:10 [build  ] Built with Go version go1.12.5
2019-12-23 12:31:10 [cmdline] mrp __G172_Run2_unlane.mro G172_Run2_unlane --localcores=12
2019-12-23 12:31:10 [pid    ] 112508
2019-12-23 12:31:10 [environ] HOSTNAME=scc-tm2.scc.bu.edu
2019-12-23 12:31:10 [environ] SGE_TASK_STEPSIZE=undefined
2019-12-23 12:31:10 [environ] SHELL=/bin/bash
2019-12-23 12:31:10 [environ] NHOSTS=1
2019-12-23 12:31:10 [environ] SGE_O_WORKDIR=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172
2019-12-23 12:31:10 [environ] TMPDIR=/scratch/1823540.1.linga
2019-12-23 12:31:10 [environ] CONDA_SHLVL=1
2019-12-23 12:31:10 [environ] SGE_O_HOME=/usr4/spclpgm/kkarri
2019-12-23 12:31:10 [environ] CONDA_PROMPT_MODIFIER=(base) 
2019-12-23 12:31:10 [environ] SGE_ARCH=linux-x64
2019-12-23 12:31:10 [environ] SGE_CELL=default
2019-12-23 12:31:10 [environ] LC_ALL=C
2019-12-23 12:31:10 [environ] PYTHONUSERBASE=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib
2019-12-23 12:31:10 [environ] USER=kkarri
2019-12-23 12:31:10 [environ] LD_LIBRARY_PATH=
2019-12-23 12:31:10 [environ] CONDA_EXE=/restricted/projectnb/waxmanlab/kkarri/miniconda3/bin/conda
2019-12-23 12:31:10 [environ] SGE_TASK_LAST=undefined
2019-12-23 12:31:10 [environ] TENX_SUBCMD=mkfastq
2019-12-23 12:31:10 [environ] TENX_PRODUCT=cellranger
2019-12-23 12:31:10 [environ] SGE_TASK_ID=undefined
2019-12-23 12:31:10 [environ] SGE_BINARY_PATH=/usr/local/ogs-ge2011.11.p1/sge_root/bin/linux-x64
2019-12-23 12:31:10 [environ] PATH=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-tiny-fastq/3.0.0:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-tiny-ref/3.0.0:/share/pkg.7/cellranger/3.1.0/install/bin/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/tenkit/lib/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/tenkit/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/bin:/share/pkg.7/cellranger/3.1.0/install/bin/lz4/v1.8.1.2:/share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/bin:/share/pkg.7/cellranger/3.1.0/install/bin/STAR/5dda596:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-tiny-fastq/3.0.0:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-tiny-ref/3.0.0:/share/pkg.7/cellranger/3.1.0/install/bin/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/tenkit/lib/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/tenkit/bin:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/bin:/share/pkg.7/cellranger/3.1.0/install/bin/lz4/v1.8.1.2:/share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/bin:/share/pkg.7/cellranger/3.1.0/install/bin/STAR/5dda596:/restricted/projectnb/waxmanlab/kkarri/miniconda3/bin:/restricted/projectnb/waxmanlab/kkarri/miniconda3/condabin:/scratch/1823540.1.linga:/share/pkg.7/cellranger/3.1.0/install/bin:/share/pkg.7/bcl2fastq/2.20/install/bin:/restricted/projectnb/waxmanlab/kkarri/miniconda3/condabin:/usr/java/default/jre/bin:/usr/java/default/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin:/bin:/usr4/spclpgm/kkarri/bin:.
2019-12-23 12:31:10 [environ] CONDA_PREFIX=/restricted/projectnb/waxmanlab/kkarri/miniconda3
2019-12-23 12:31:10 [environ] SGE_STDERR_PATH=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/bcl2fastq_G172_run2_unlane.log
2019-12-23 12:31:10 [environ] PWD=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172
2019-12-23 12:31:10 [environ] SGE_STDOUT_PATH=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/bcl2fastq_G172_run2_unlane.log
2019-12-23 12:31:10 [environ] SGE_ACCOUNT=sge
2019-12-23 12:31:10 [environ] LANG=C
2019-12-23 12:31:10 [environ] JOB_SCRIPT=/var/spool/sge/scc-tm2/job_scripts/1823540
2019-12-23 12:31:10 [environ] JOB_NAME=bcl2fastq_G172_run2_unlane
2019-12-23 12:31:10 [environ] SGE_ROOT=/usr/local/sge/sge_root
2019-12-23 12:31:10 [environ] SGE_JOB_SPOOL_DIR=/var/spool/sge/scc-tm2/active_jobs/1823540.1
2019-12-23 12:31:10 [environ] ENVIRONMENT=BATCH
2019-12-23 12:31:10 [environ] SHLVL=3
2019-12-23 12:31:10 [environ] HOME=/usr4/spclpgm/kkarri
2019-12-23 12:31:10 [environ] TENX_COPYRIGHT=Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
2019-12-23 12:31:10 [environ] SGE_CWD_PATH=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172
2019-12-23 12:31:10 [environ] NQUEUES=1
2019-12-23 12:31:10 [environ] SGE_O_LOGNAME=kkarri
2019-12-23 12:31:10 [environ] SGE_O_MAIL=/var/spool/mail/kkarri
2019-12-23 12:31:10 [environ] PYTHONPATH=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/tenkit/lib/python:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/python:/share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/adapters/python
2019-12-23 12:31:10 [environ] CONDA_PYTHON_EXE=/restricted/projectnb/waxmanlab/kkarri/miniconda3/bin/python
2019-12-23 12:31:10 [environ] JOB_ID=1823540
2019-12-23 12:31:10 [environ] LOGNAME=kkarri
2019-12-23 12:31:10 [environ] TENX_SCRIPTDIR=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/bin
2019-12-23 12:31:10 [environ] TENX_BANNER=cellranger mkfastq (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------
2019-12-23 12:31:10 [environ] XDG_DATA_DIRS=/usr4/spclpgm/kkarri/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
2019-12-23 12:31:10 [environ] SGE_TASK_FIRST=undefined
2019-12-23 12:31:10 [environ] TENX_VERSION=3.1.0
2019-12-23 12:31:10 [environ] CONDA_DEFAULT_ENV=base
2019-12-23 12:31:10 [environ] SGE_O_PATH=/share/pkg.7/cellranger/3.1.0/install/bin:/share/pkg.7/bcl2fastq/2.20/install/bin:/restricted/projectnb/waxmanlab/kkarri/miniconda3/condabin:/usr/java/default/jre/bin:/usr/java/default/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin:/bin:/usr4/spclpgm/kkarri/bin:.
2019-12-23 12:31:10 [environ] SGE_O_HOST=scc4
2019-12-23 12:31:10 [environ] SGE_O_SHELL=/bin/bash
2019-12-23 12:31:10 [environ] NSLOTS=16
2019-12-23 12:31:10 [environ] SGE_STDIN_PATH=/dev/null
2019-12-23 12:31:10 [environ] BASH_FUNC_module()=() {  eval `/usr/local/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
2019-12-23 12:31:10 [environ] _=/share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/bin/mrp
2019-12-23 12:31:10 [environ] MROFLAGS=--vdrmode=rolling
2019-12-23 12:31:10 [options] --localcores=12
2019-12-23 12:31:10 [environ] MROPATH=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/tenkit/mro:/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/mro
2019-12-23 12:31:10 [version] MRO Version=3.1.0
2019-12-23 12:31:10 [options] --jobmode=local
2019-12-23 12:31:10 [options] --maxjobs=0
2019-12-23 12:31:10 [options] --jobinterval=0
2019-12-23 12:31:10 [options] --vdrmode=rolling
2019-12-23 12:31:10 [options] --stackvars=false
2019-12-23 12:31:10 [options] --zip=false
2019-12-23 12:31:10 [options] --limit-loadavg=false
2019-12-23 12:31:10 [options] --noexit=false
2019-12-23 12:31:10 [options] --nopreflight=false
2019-12-23 12:31:10 [jobmngr] Job config = /share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/jobmanagers/config.json
2019-12-23 12:31:10 [jobmngr] Using 12 cores, per --localcores option.
2019-12-23 12:31:10 [jobmngr] Using 226 GB, 90% of system memory.
2019-12-23 12:31:10 [filesys] Pipestance path /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/G172_Run2_unlane
2019-12-23 12:31:10 [filesys] Pipestance filesystem type nfs
2019-12-23 12:31:10 [filesys] 22 TB and 1,089,442,601 inodes available.
2019-12-23 12:31:10 [filesys] Pipestance filesystem nfs mount options: rw,nosuid,nodev,relatime,rw,vers=3,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=10.241.29.116,mountvers=3,mountport=20048,mountproto=tcp,local_lock=none,addr=10.241.29.116
2019-12-23 12:31:10 [filesys] Bin path /share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/bin
2019-12-23 12:31:10 [filesys] Bin filesystem type nfs
2019-12-23 12:31:10 [filesys] Bin filesystem nfs mount options: rw,nosuid,nodev,relatime,rw,vers=3,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=192.168.16.24,mountvers=3,mountport=890,mountproto=udp,local_lock=none,addr=192.168.16.24
Serving UI at http://scc-tm2:41812?auth=ug6c3ojpv1BO1qKHmj_1JAeoTEPigNlL5sB6brmLjDo

Running preflight checks (please wait)...
2019-12-23 12:31:11 [runtime] (ready)           ID.G172_Run2_unlane.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL
2019-12-23 12:31:11 [runtime] (run:local)       ID.G172_Run2_unlane.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL.fork0.chnk0.main
2019-12-23 12:31:11 [runtime] (ready)           ID.G172_Run2_unlane.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT
2019-12-23 12:31:13 [runtime] (run:local)       ID.G172_Run2_unlane.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT.fork0.chnk0.main
2019-12-23 12:31:15 [runtime] (chunks_complete) ID.G172_Run2_unlane.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT
2019-12-23 12:31:16 [runtime] (failed)          ID.G172_Run2_unlane.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL

[error] Formatting error in sample sheet: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/G172_v2.csv

2019-12-23 12:31:16 Shutting down.
Waiting 6 seconds for UI to do final refresh.
2019-12-23 12:31:16 [jobmngr] Highest memory usage observed: {
  "rss": 52518912,
  "shared": 12922880,
  "vmem": 493584384,
  "text": 4599808,
  "stack": 319602688,
  "proc_count": 23
}
