Martian Runtime - '3.1.0-v3.2.3'
2019-10-01 11:18:31 [build  ] Built with Go version go1.12.5
2019-10-01 11:18:31 [cmdline] mrp __h2b_run2.mro h2b_run2
2019-10-01 11:18:31 [pid    ] 34280
2019-10-01 11:18:31 [environ] SLURM_NODELIST=c2a-s12
2019-10-01 11:18:31 [environ] SLURM_JOB_NAME=cellrangercount
2019-10-01 11:18:31 [environ] XDG_SESSION_ID=299854
2019-10-01 11:18:31 [environ] SLURM_TOPOLOGY_ADDR=ibswt1-1.ibswt2-4.ibswc0b.ibswc2a.c2a-s12
2019-10-01 11:18:31 [environ] HOSTNAME=c2a-s12
2019-10-01 11:18:31 [environ] SLURM_PRIO_PROCESS=0
2019-10-01 11:18:31 [environ] SLURM_NODE_ALIASES=(null)
2019-10-01 11:18:31 [environ] TERM=xterm-256color
2019-10-01 11:18:31 [environ] SHELL=/bin/bash
2019-10-01 11:18:31 [environ] SLURM_JOB_QOS=ewang burst qos
2019-10-01 11:18:31 [environ] TMPDIR=/scratch/local/42029954
2019-10-01 11:18:31 [environ] SLURM_TOPOLOGY_ADDR_PATTERN=switch.switch.switch.switch.node
2019-10-01 11:18:31 [environ] SSH_CLIENT=10.16.65.40 52603 22
2019-10-01 11:18:31 [environ] SSH_TTY=/dev/pts/136
2019-10-01 11:18:31 [environ] LC_ALL=C
2019-10-01 11:18:31 [environ] SLURM_MEM_PER_CPU=40960
2019-10-01 11:18:31 [environ] PYTHONUSERBASE=/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib
2019-10-01 11:18:31 [environ] SLURM_NNODES=1
2019-10-01 11:18:31 [environ] USER=lancetdenes
2019-10-01 11:18:31 [environ] LD_LIBRARY_PATH=
2019-10-01 11:18:31 [environ] TENX_SUBCMD=count
2019-10-01 11:18:31 [environ] SLURM_JOBID=42029954
2019-10-01 11:18:31 [environ] TENX_PRODUCT=cellranger
2019-10-01 11:18:31 [environ] SLURM_NTASKS=1
2019-10-01 11:18:31 [environ] SLURM_TASKS_PER_NODE=1
2019-10-01 11:18:31 [environ] PATH=/apps/cellranger/3.1.0/cellranger-tiny-fastq/3.0.0:/apps/cellranger/3.1.0/cellranger-tiny-ref/3.0.0:/apps/cellranger/3.1.0/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/tenkit/lib/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/tenkit/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/bin:/apps/cellranger/3.1.0/lz4/v1.8.1.2:/apps/cellranger/3.1.0/martian-cs/v3.2.3/bin:/apps/cellranger/3.1.0/STAR/5dda596:/apps/cellranger/3.1.0/cellranger-tiny-fastq/3.0.0:/apps/cellranger/3.1.0/cellranger-tiny-ref/3.0.0:/apps/cellranger/3.1.0/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/tenkit/lib/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/tenkit/bin:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/bin:/apps/cellranger/3.1.0/lz4/v1.8.1.2:/apps/cellranger/3.1.0/martian-cs/v3.2.3/bin:/apps/cellranger/3.1.0/STAR/5dda596:/apps/cellranger/3.1.0:/apps/gcc/5.2.0/bcl2fastq/2.20.0.422/bin:/apps/compilers/gcc/5.2.0/bin:/apps/maven/3.5.0/bin:/apps/java/jdk-9.0.1/ant/bin:/apps/java/jdk-9.0.1/bin:/apps/ufrc/share/man:/apps/ufrc/bin:/home/lancetdenes/.local/bin:/opt/slurm/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/bin:/opt/dell/srvadmin/bin
2019-10-01 11:18:31 [environ] SLURM_WORKING_CLUSTER=hipergator:vslurm:6817:8704:109
2019-10-01 11:18:31 [environ] SLURM_JOB_ID=42029954
2019-10-01 11:18:31 [environ] SLURM_CPUS_PER_TASK=4
2019-10-01 11:18:31 [environ] SLURM_JOB_USER=lancetdenes
2019-10-01 11:18:31 [environ] PWD=/ufrc/ewang/lancetdenes/libLTD
2019-10-01 11:18:31 [environ] JAVA_HOME=/apps/java/jdk-9.0.1
2019-10-01 11:18:31 [environ] LANG=en_US.UTF-8
2019-10-01 11:18:31 [environ] SLURM_JOB_UID=4180
2019-10-01 11:18:31 [environ] SLURM_NODEID=0
2019-10-01 11:18:31 [environ] SLURM_SUBMIT_DIR=/ufrc/ewang/lancetdenes/libLTD
2019-10-01 11:18:31 [environ] SLURM_TASK_PID=33211
2019-10-01 11:18:31 [environ] SLURM_NPROCS=1
2019-10-01 11:18:31 [environ] SLURM_CPUS_ON_NODE=4
2019-10-01 11:18:31 [environ] SLURM_PROCID=0
2019-10-01 11:18:31 [environ] ENVIRONMENT=BATCH
2019-10-01 11:18:31 [environ] SLURM_JOB_NODELIST=c2a-s12
2019-10-01 11:18:31 [environ] TENX_REFDATA=/ufrc/data/reference/cellranger/latest
2019-10-01 11:18:31 [environ] SHLVL=5
2019-10-01 11:18:31 [environ] HOME=/home/lancetdenes
2019-10-01 11:18:31 [environ] TENX_COPYRIGHT=Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
2019-10-01 11:18:31 [environ] SLURM_LOCALID=0
2019-10-01 11:18:31 [environ] SLURM_JOB_GID=3517
2019-10-01 11:18:31 [environ] SLURM_JOB_CPUS_PER_NODE=4
2019-10-01 11:18:31 [environ] SLURM_CLUSTER_NAME=hipergator
2019-10-01 11:18:31 [environ] SLURM_GTIDS=0
2019-10-01 11:18:31 [environ] SLURM_SUBMIT_HOST=login1.ufhpc
2019-10-01 11:18:31 [environ] SLURM_JOB_PARTITION=hpg1-compute
2019-10-01 11:18:31 [environ] BASH_ENV=/apps/lmod/lmod/init/bash
2019-10-01 11:18:31 [environ] PYTHONPATH=/apps/cellranger/3.1.0/cellranger-cs/3.1.0/tenkit/lib/python:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/python:/apps/cellranger/3.1.0/martian-cs/v3.2.3/adapters/python
2019-10-01 11:18:31 [environ] LOGNAME=lancetdenes
2019-10-01 11:18:31 [environ] SLURM_TMPDIR=/scratch/local/42029954
2019-10-01 11:18:31 [environ] TENX_SCRIPTDIR=/apps/cellranger/3.1.0/cellranger-cs/3.1.0/bin
2019-10-01 11:18:31 [environ] TENX_BANNER=cellranger count (3.1.0)
Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------
2019-10-01 11:18:31 [environ] SLURM_JOB_ACCOUNT=ewang
2019-10-01 11:18:31 [environ] SSH_CONNECTION=10.16.65.40 52603 10.13.55.16 22
2019-10-01 11:18:31 [environ] SLURM_JOB_NUM_NODES=1
2019-10-01 11:18:31 [environ] TENX_VERSION=3.1.0
2019-10-01 11:18:31 [environ] XDG_RUNTIME_DIR=/run/user/4180
2019-10-01 11:18:31 [environ] BASH_FUNC_module()=() {  eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
2019-10-01 11:18:31 [environ] BASH_FUNC_ml()=() {  eval $($LMOD_DIR/ml_cmd "$@")
}
2019-10-01 11:18:31 [environ] _=/apps/cellranger/3.1.0/martian-cs/v3.2.3/bin/mrp
2019-10-01 11:18:31 [environ] MROFLAGS=--vdrmode=rolling
2019-10-01 11:18:31 [environ] MROPATH=/apps/cellranger/3.1.0/cellranger-cs/3.1.0/tenkit/mro:/apps/cellranger/3.1.0/cellranger-cs/3.1.0/mro
2019-10-01 11:18:31 [version] MRO Version=3.1.0
2019-10-01 11:18:31 [options] --jobmode=local
2019-10-01 11:18:31 [options] --maxjobs=0
2019-10-01 11:18:31 [options] --jobinterval=0
2019-10-01 11:18:31 [options] --vdrmode=rolling
2019-10-01 11:18:31 [options] --stackvars=false
2019-10-01 11:18:31 [options] --zip=false
2019-10-01 11:18:31 [options] --limit-loadavg=false
2019-10-01 11:18:31 [options] --noexit=false
2019-10-01 11:18:31 [options] --nopreflight=false
2019-10-01 11:18:31 [jobmngr] Job config = /apps/cellranger/3.1.0/martian-cs/v3.2.3/jobmanagers/config.json
2019-10-01 11:18:31 [jobmngr] Using 4 logical cores available on system.
2019-10-01 11:18:31 [jobmngr] Detected cgroup memory limit of 171798691840 bytes.  Using it instead of total system memory 270296305664
2019-10-01 11:18:31 [jobmngr] Using 153 GB, 96% of system memory.
2019-10-01 11:18:32 [filesys] Pipestance path /ufrc/ewang/lancetdenes/libLTD/h2b_run2
2019-10-01 11:18:32 [filesys] Pipestance filesystem type lustre
2019-10-01 11:18:32 [filesys] 549 TB and 1,657,247,082 inodes available.
2019-10-01 11:18:32 [filesys] Pipestance filesystem lustre mount options: rw,rw,localflock,lazystatfs
2019-10-01 11:18:32 [filesys] Bin path /apps/cellranger/3.1.0/martian-cs/v3.2.3/bin
2019-10-01 11:18:32 [filesys] Bin filesystem type nfs
2019-10-01 11:18:32 [filesys] Bin filesystem nfs mount options: rw,relatime,rw,vers=3,rsize=1048576,wsize=1048576,namlen=255,hard,noacl,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=10.13.152.217,mountvers=3,mountport=2049,mountproto=tcp,local_lock=none,addr=10.13.152.217
Serving UI at http://c2a-s12.ufhpc:33847?auth=U0eTW1MozsyvHdeD2rfCr-psibHm-CZ1AtAUr7c1_9A

Running preflight checks (please wait)...
2019-10-01 11:18:32 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF
2019-10-01 11:18:32 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF.fork0.chnk0.main
2019-10-01 11:18:45 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.EXPAND_SAMPLE_DEF
2019-10-01 11:18:45 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT
2019-10-01 11:18:45 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT.fork0.chnk0.main
2019-10-01 11:18:45 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT_LOCAL
2019-10-01 11:18:45 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT_LOCAL.fork0.chnk0.main
2019-10-01 11:19:04 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT_LOCAL
2019-10-01 11:19:09 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CELLRANGER_PREFLIGHT
2019-10-01 11:19:09 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY
2019-10-01 11:19:09 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0.main
2019-10-01 11:19:09 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES
2019-10-01 11:19:09 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES.fork0.chnk0.main
2019-10-01 11:19:09 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION
2019-10-01 11:19:09 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION.fork0.chnk0.main
2019-10-01 11:19:10 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.DISABLE_FEATURE_STAGES
2019-10-01 11:19:10 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION
2019-10-01 11:19:19 [runtime] (progress)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Building transcriptome...
2019-10-01 11:21:41 [runtime] (progress)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Building kmer index...
2019-10-01 11:23:05 [runtime] (progress)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Mapping reads...
2019-10-01 11:23:32 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY
2019-10-01 11:23:32 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
2019-10-01 11:23:32 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS.fork0.chnk0.main
2019-10-01 11:23:39 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
2019-10-01 11:23:39 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS
2019-10-01 11:23:39 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS.fork0.split
2019-10-01 11:23:39 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHECK_BARCODES_COMPATIBILITY
2019-10-01 11:23:39 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHECK_BARCODES_COMPATIBILITY.fork0.split
2019-10-01 11:23:40 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS
2019-10-01 11:23:40 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS.fork0.chnk0.main
2019-10-01 11:23:40 [jobmngr] Need 4 threads to start the next job (3 available).  Waiting for jobs to complete.
2019-10-01 11:23:46 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHECK_BARCODES_COMPATIBILITY
2019-10-01 11:23:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHECK_BARCODES_COMPATIBILITY.fork0.join
2019-10-01 11:29:49 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS.fork0 chunks_running
2019-10-01 11:34:36 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS
2019-10-01 11:34:36 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS.fork0.join
2019-10-01 11:34:37 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHECK_BARCODES_COMPATIBILITY.fork0 join_running
2019-10-01 11:34:37 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.CHUNK_READS
2019-10-01 11:34:37 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS
2019-10-01 11:34:37 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.split
2019-10-01 11:34:44 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHECK_BARCODES_COMPATIBILITY
2019-10-01 11:34:46 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk00.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk01.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk02.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk03.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk04.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk05.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk06.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk07.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk08.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk09.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk10.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk11.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk12.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk13.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk14.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk15.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk16.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk17.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk18.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk19.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk20.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk21.main
2019-10-01 11:34:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.EXTRACT_READS.fork0.chnk22.main
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2019-10-02 07:43:19 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (1/40 completed)
2019-10-02 07:48:19 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (5/40 completed)
2019-10-02 07:53:39 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (8/40 completed)
2019-10-02 07:58:47 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (12/40 completed)
2019-10-02 08:03:49 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (15/40 completed)
2019-10-02 08:09:12 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (17/40 completed)
2019-10-02 08:14:28 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (21/40 completed)
2019-10-02 08:20:01 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (25/40 completed)
2019-10-02 08:25:05 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (28/40 completed)
2019-10-02 08:31:02 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (32/40 completed)
2019-10-02 08:36:26 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (36/40 completed)
2019-10-02 08:37:37 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.PREPROCESS_MATRIX.fork0 split_running
2019-10-02 08:37:43 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.PREPROCESS_MATRIX
2019-10-02 08:37:43 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.PREPROCESS_MATRIX.fork0.join
2019-10-02 08:38:02 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.PREPROCESS_MATRIX
2019-10-02 08:38:02 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA
2019-10-02 08:38:02 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA.fork0.split
2019-10-02 08:38:02 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_FBPCA
2019-10-02 08:38:02 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_FBPCA
2019-10-02 08:38:02 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS
2019-10-02 08:38:02 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS.fork0.split
2019-10-02 08:38:02 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH
2019-10-02 08:38:02 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH
2019-10-02 08:38:10 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA
2019-10-02 08:38:10 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA.fork0.chnk0.main
2019-10-02 08:38:18 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS
2019-10-02 08:38:18 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS.fork0.join
2019-10-02 08:38:46 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA
2019-10-02 08:38:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA.fork0.join
2019-10-02 08:38:54 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS
2019-10-02 08:38:59 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_PCA
2019-10-02 08:38:59 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION_OUTPUT
2019-10-02 08:38:59 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION_OUTPUT.fork0.chnk0.main
2019-10-02 08:39:04 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION_OUTPUT
2019-10-02 08:39:04 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP
2019-10-02 08:39:04 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP.fork0.split
2019-10-02 08:39:04 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE
2019-10-02 08:39:04 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE.fork0.split
2019-10-02 08:39:04 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING
2019-10-02 08:39:04 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING.fork0.split
2019-10-02 08:39:04 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS
2019-10-02 08:39:04 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.split
2019-10-02 08:39:13 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE
2019-10-02 08:39:13 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE.fork0.chnk0.main
2019-10-02 08:39:20 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP
2019-10-02 08:39:20 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP.fork0.chnk0.main
2019-10-02 08:39:21 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING
2019-10-02 08:39:21 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING.fork0.chnk0.main
2019-10-02 08:39:29 [jobmngr] Need 4 threads to start the next job (1 available).  Waiting for jobs to complete.
2019-10-02 08:39:30 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk0.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk1.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk2.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk3.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk4.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk5.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk6.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk7.main
2019-10-02 08:39:30 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk8.main
2019-10-02 08:40:08 [jobmngr] Need 4 threads to start the next job (2 available).  Waiting for jobs to complete.
2019-10-02 08:40:08 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE
2019-10-02 08:40:08 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE.fork0.join
2019-10-02 08:41:36 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0 chunks running (38/40 completed)
2019-10-02 08:41:50 [jobmngr] Need 4 threads to start the next job (3 available).  Waiting for jobs to complete.
2019-10-02 08:41:55 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES
2019-10-02 08:41:55 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES.fork0.join
2019-10-02 08:42:59 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP
2019-10-02 08:42:59 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP.fork0.join
2019-10-02 08:43:11 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING
2019-10-02 08:43:11 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING.fork0.join
2019-10-02 08:43:31 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_TSNE
2019-10-02 08:43:35 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS
2019-10-02 08:43:35 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS.fork0.join
2019-10-02 08:43:44 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_KMEANS
2019-10-02 08:43:47 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_UMAP
2019-10-02 08:44:01 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING
2019-10-02 08:44:01 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS
2019-10-02 08:44:01 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS.fork0.split
2019-10-02 08:44:10 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS
2019-10-02 08:44:10 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS.fork0.chnk0.main
2019-10-02 08:44:18 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS
2019-10-02 08:44:18 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS.fork0.join
2019-10-02 08:44:47 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.MERGE_CLUSTERS
2019-10-02 08:44:47 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.COMBINE_CLUSTERING
2019-10-02 08:44:48 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.COMBINE_CLUSTERING.fork0.chnk0.main
2019-10-02 08:44:53 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.COMBINE_CLUSTERING
2019-10-02 08:44:53 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
2019-10-02 08:44:53 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.split
2019-10-02 08:45:00 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk00.main
2019-10-02 08:45:00 [jobmngr] Need 4 threads to start the next job (3 available).  Waiting for jobs to complete.
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk01.main
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk02.main
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk03.main
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk04.main
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk05.main
2019-10-02 08:45:00 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk06.main
2019-10-02 08:45:01 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk07.main
2019-10-02 08:45:01 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk08.main
2019-10-02 08:45:01 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk09.main
2019-10-02 08:46:59 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.REPORT_MOLECULES
2019-10-02 08:47:05 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS
2019-10-02 08:47:05 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS.fork0.split
2019-10-02 08:50:37 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0 chunks running (2/10 completed)
2019-10-02 08:56:52 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0 chunks running (9/10 completed)
2019-10-02 08:58:29 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
2019-10-02 08:58:29 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.join
2019-10-02 08:58:32 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS.fork0 split_running
2019-10-02 08:58:39 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS
2019-10-02 08:58:39 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS.fork0.chnk0.main
2019-10-02 08:58:40 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
2019-10-02 08:58:41 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2019-10-02 08:58:41 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork0.split
2019-10-02 08:58:46 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2019-10-02 08:58:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork0.chnk0.main
2019-10-02 08:58:55 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2019-10-02 08:58:55 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork0.join
2019-10-02 08:59:01 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2019-10-02 09:04:40 [runtime] (update)          ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS.fork0 chunks_running
2019-10-02 09:06:23 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS
2019-10-02 09:06:23 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS.fork0.join
2019-10-02 09:06:33 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUBSAMPLE_READS
2019-10-02 09:06:33 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS
2019-10-02 09:06:33 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS.fork0.split
2019-10-02 09:06:40 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS
2019-10-02 09:06:40 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS.fork0.chnk0.main
2019-10-02 09:06:47 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS
2019-10-02 09:06:47 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS.fork0.join
2019-10-02 09:06:54 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.SUMMARIZE_BASIC_REPORTS
2019-10-02 09:06:58 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER.CALL_PROTOSPACERS
2019-10-02 09:06:58 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER.CALL_PROTOSPACERS
2019-10-02 09:06:59 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE
2019-10-02 09:06:59 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE
2019-10-02 09:06:59 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SUMMARIZE_REPORTS
2019-10-02 09:06:59 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SUMMARIZE_REPORTS.fork0.chnk0.main
2019-10-02 09:06:59 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET
2019-10-02 09:06:59 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET
2019-10-02 09:06:59 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS
2019-10-02 09:06:59 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS
2019-10-02 09:06:59 [runtime] (disabled)        ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._CRISPR_ANALYZER
2019-10-02 09:07:39 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SUMMARIZE_REPORTS
2019-10-02 09:07:39 [runtime] (ready)           ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS
2019-10-02 09:07:39 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.split
2019-10-02 09:07:46 [runtime] (split_complete)  ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS
2019-10-02 09:07:46 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.main
2019-10-02 09:08:12 [runtime] (chunks_complete) ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS
2019-10-02 09:08:12 [runtime] (run:local)       ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.join
2019-10-02 09:08:18 [runtime] (join_complete)   ID.h2b_run2.SC_RNA_COUNTER_CS.CLOUPE_PREPROCESS
2019-10-02 09:08:19 [runtime] VDR killed 2232 files, 234 GB.

Outputs:
- Run summary HTML:                         /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/web_summary.html
- Run summary CSV:                          /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/metrics_summary.csv
- BAM:                                      /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/possorted_genome_bam.bam
- BAM index:                                /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/possorted_genome_bam.bam.bai
- Filtered feature-barcode matrices MEX:    /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/filtered_feature_bc_matrix
- Filtered feature-barcode matrices HDF5:   /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/filtered_feature_bc_matrix.h5
- Unfiltered feature-barcode matrices MEX:  /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/raw_feature_bc_matrix
- Unfiltered feature-barcode matrices HDF5: /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/raw_feature_bc_matrix.h5
- Secondary analysis output CSV:            /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/analysis
- Per-molecule read information:            /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/molecule_info.h5
- CRISPR-specific analysis:                 null
- Loupe Cell Browser file:                  /ufrc/ewang/lancetdenes/libLTD/h2b_run2/outs/cloupe.cloupe
- Feature Reference:                        null

2019-10-02 09:08:20 [perform] Serializing pipestance performance data.
Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!

2019-10-02 09:08:26 Shutting down.
2019-10-02 09:08:26 [jobmngr] Highest memory usage observed: {
  "rss": 12910030848,
  "shared": 115834880,
  "vmem": 15098343424,
  "text": 17281024,
  "stack": 13746032640,
  "proc_count": 325
}
