Martian Runtime - '3.1.0-v3.2.3'
2019-09-18 12:30:15 [build  ] Built with Go version go1.12.5
2019-09-18 12:30:15 [cmdline] mrp __10X_G171B_ERCC.mro 10X_G171B_ERCC
2019-09-18 12:30:15 [pid    ] 18717
2019-09-18 12:30:15 [environ] HOSTNAME=scc-wk1.scc.bu.edu
2019-09-18 12:30:15 [environ] SGE_TASK_STEPSIZE=undefined
2019-09-18 12:30:15 [environ] SHELL=/bin/bash
2019-09-18 12:30:15 [environ] NHOSTS=1
2019-09-18 12:30:15 [environ] SGE_O_WORKDIR=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171
2019-09-18 12:30:15 [environ] TMPDIR=/scratch/9423894.1.mem512
2019-09-18 12:30:15 [environ] SGE_O_HOME=/usr4/spclpgm/kkarri
2019-09-18 12:30:15 [environ] SGE_ARCH=linux-x64
2019-09-18 12:30:15 [environ] SGE_CELL=default
2019-09-18 12:30:15 [environ] LC_ALL=C
2019-09-18 12:30:15 [environ] PYTHONUSERBASE=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib
2019-09-18 12:30:15 [environ] USER=kkarri
2019-09-18 12:30:15 [environ] LD_LIBRARY_PATH=
2019-09-18 12:30:15 [environ] SGE_TASK_LAST=undefined
2019-09-18 12:30:15 [environ] TENX_SUBCMD=count
2019-09-18 12:30:15 [environ] TENX_PRODUCT=cellranger
2019-09-18 12:30:15 [environ] SGE_TASK_ID=undefined
2019-09-18 12:30:15 [environ] SGE_BINARY_PATH=/usr/local/ogs-ge2011.11.p1/sge_root/bin/linux-x64
2019-09-18 12:30:15 [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:/share/pkg.7/cellranger/3.1.0/install/bin:/share/pkg.7/bcl2fastq/2.20/install/bin:/scratch/9423894.1.mem512:/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:.
2019-09-18 12:30:15 [environ] SGE_STDERR_PATH=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/mm10_10X_G171B_ERCC_omp28.o9423894
2019-09-18 12:30:15 [environ] PWD=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171
2019-09-18 12:30:15 [environ] SGE_STDOUT_PATH=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/mm10_10X_G171B_ERCC_omp28.o9423894
2019-09-18 12:30:15 [environ] SGE_ACCOUNT=sge
2019-09-18 12:30:15 [environ] LANG=C
2019-09-18 12:30:15 [environ] JOB_SCRIPT=/var/spool/sge/scc-wk1/job_scripts/9423894
2019-09-18 12:30:15 [environ] JOB_NAME=mm10_10X_G171B_ERCC_omp28
2019-09-18 12:30:15 [environ] SGE_ROOT=/usr/local/sge/sge_root
2019-09-18 12:30:15 [environ] SGE_JOB_SPOOL_DIR=/var/spool/sge/scc-wk1/active_jobs/9423894.1
2019-09-18 12:30:15 [environ] ENVIRONMENT=BATCH
2019-09-18 12:30:15 [environ] SHLVL=3
2019-09-18 12:30:15 [environ] HOME=/usr4/spclpgm/kkarri
2019-09-18 12:30:15 [environ] TENX_COPYRIGHT=Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
2019-09-18 12:30:15 [environ] SGE_CWD_PATH=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171
2019-09-18 12:30:15 [environ] NQUEUES=1
2019-09-18 12:30:15 [environ] SGE_O_LOGNAME=kkarri
2019-09-18 12:30:15 [environ] SGE_O_MAIL=/var/spool/mail/kkarri
2019-09-18 12:30:15 [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
2019-09-18 12:30:15 [environ] JOB_ID=9423894
2019-09-18 12:30:15 [environ] LOGNAME=kkarri
2019-09-18 12:30:15 [environ] TENX_SCRIPTDIR=/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/bin
2019-09-18 12:30:15 [environ] TENX_BANNER=cellranger count (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------
2019-09-18 12:30:15 [environ] XDG_DATA_DIRS=/usr4/spclpgm/kkarri/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
2019-09-18 12:30:15 [environ] SGE_TASK_FIRST=undefined
2019-09-18 12:30:15 [environ] TENX_VERSION=3.1.0
2019-09-18 12:30:15 [environ] SGE_O_PATH=/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:.
2019-09-18 12:30:15 [environ] SGE_O_HOST=scc4
2019-09-18 12:30:15 [environ] SGE_O_SHELL=/bin/bash
2019-09-18 12:30:15 [environ] NSLOTS=28
2019-09-18 12:30:15 [environ] SGE_STDIN_PATH=/dev/null
2019-09-18 12:30:15 [environ] BASH_FUNC_module()=() {  eval `/usr/local/Modules/$MODULE_VERSION/bin/modulecmd bash $*`
}
2019-09-18 12:30:15 [environ] _=/share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/bin/mrp
2019-09-18 12:30:15 [environ] MROFLAGS=--vdrmode=rolling
2019-09-18 12:30:15 [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
2019-09-18 12:30:15 [version] MRO Version=3.1.0
2019-09-18 12:30:15 [options] --jobmode=local
2019-09-18 12:30:15 [options] --maxjobs=0
2019-09-18 12:30:15 [options] --jobinterval=0
2019-09-18 12:30:15 [options] --vdrmode=rolling
2019-09-18 12:30:15 [options] --stackvars=false
2019-09-18 12:30:15 [options] --zip=false
2019-09-18 12:30:15 [options] --limit-loadavg=false
2019-09-18 12:30:15 [options] --noexit=false
2019-09-18 12:30:15 [options] --nopreflight=false
2019-09-18 12:30:15 [jobmngr] Job config = /share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/jobmanagers/config.json
2019-09-18 12:30:15 [jobmngr] Using 28 logical cores available on system.
2019-09-18 12:30:15 [jobmngr] Using 453 GB, 90% of system memory.
2019-09-18 12:30:16 [filesys] Pipestance path /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_ERCC
2019-09-18 12:30:16 [filesys] Pipestance filesystem type nfs
2019-09-18 12:30:16 [filesys] 25 TB and 1,089,563,564 inodes available.
2019-09-18 12:30:16 [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
2019-09-18 12:30:16 [filesys] Bin path /share/pkg.7/cellranger/3.1.0/install/bin/martian-cs/v3.2.3/bin
2019-09-18 12:30:16 [filesys] Bin filesystem type nfs
2019-09-18 12:30:16 [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=192.168.16.27,mountvers=3,mountport=890,mountproto=udp,local_lock=none,addr=192.168.16.27
Serving UI at http://scc-wk1:38602?auth=OwaRySiEfP2fNEbbDJQuB568BLauQdcmSbKX_0nil0w

Running preflight checks (please wait)...
2019-09-18 12:30:16 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF
2019-09-18 12:30:17 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF.fork0.chnk0.main
2019-09-18 12:30:23 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF
2019-09-18 12:30:24 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT_LOCAL
2019-09-18 12:30:24 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT_LOCAL.fork0.chnk0.main
2019-09-18 12:30:24 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT
2019-09-18 12:30:25 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT.fork0.chnk0.main
2019-09-18 12:30:29 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT_LOCAL
2019-09-18 12:30:30 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT
2019-09-18 12:30:31 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION
2019-09-18 12:30:32 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION.fork0.chnk0.main
2019-09-18 12:30:32 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES
2019-09-18 12:30:33 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES.fork0.chnk0.main
2019-09-18 12:30:33 [runtime] (ready)           ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY
2019-09-18 12:30:34 [runtime] (run:local)       ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0.main
2019-09-18 12:30:35 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION
2019-09-18 12:30:36 [runtime] (chunks_complete) ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES
2019-09-18 12:30:39 [runtime] (progress)        ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Mapping reads...
2019-09-18 12:30:40 [runtime] (failed)          ID.10X_G171B_ERCC.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY

[error] Unable to detect the chemistry for the following dataset. Please validate it and/or specify the chemistry via the --chemistry argument.

Detect Report -- /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/H3LTJBBXX/10X_G171B_MissingLibrary_1_H3LTJBBXX (None):

R1 Total Reads:                    10000
R1 Sense Reads:                        0
R1 Antisense Reads:                   30
R2 Total Reads:                    10000
R2 Sense Reads:                        1
R2 Antisense Reads:                    1

There was not enough information to determine the nature of the library.

2019-09-18 12:30:40 Shutting down.
Waiting 6 seconds for UI to do final refresh.
2019-09-18 12:30:40 [jobmngr] Highest memory usage observed: {
  "rss": 213966848,
  "shared": 55037952,
  "vmem": 1857060864,
  "text": 4599808,
  "stack": 710418432,
  "proc_count": 41
}
