Martian Runtime - v4.0.6
2022-04-19 16:30:37 [build  ] Built with Go version go1.16.5
2022-04-19 16:30:37 [cmdline] mrp __dimitri_force_10k.mro dimitri_force_10k --jobmode local
2022-04-19 16:30:37 [pid    ] 1362430
2022-04-19 16:30:37 [environ] SHELL=/bin/bash
2022-04-19 16:30:37 [environ] CONDA_EXE=/vol/mbconda/etanis/bin/conda
2022-04-19 16:30:37 [environ] CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
2022-04-19 16:30:37 [environ] PWD=/scratch/etanis/software/cellranger-6.1.2
2022-04-19 16:30:37 [environ] LOGNAME=etanis
2022-04-19 16:30:37 [environ] XDG_SESSION_TYPE=tty
2022-04-19 16:30:37 [environ] CONDA_PREFIX=/vol/mbconda/etanis
2022-04-19 16:30:37 [environ] CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
2022-04-19 16:30:37 [environ] HOME=/home/etanis
2022-04-19 16:30:37 [environ] LANG=C
2022-04-19 16:30:37 [environ] CONDA_PROMPT_MODIFIER=(base) 
2022-04-19 16:30:37 [environ] LD=/vol/mbconda/etanis/bin/x86_64-conda-linux-gnu-ld
2022-04-19 16:30:37 [environ] SSH_CONNECTION=131.174.27.42 53824 131.174.136.191 22
2022-04-19 16:30:37 [environ] XDG_CACHE_HOME=/scratch/etanis/.cache
2022-04-19 16:30:37 [environ] XDG_SESSION_CLASS=user
2022-04-19 16:30:37 [environ] TERM=screen
2022-04-19 16:30:37 [environ] HOST=x86_64-conda-linux-gnu
2022-04-19 16:30:37 [environ] USER=etanis
2022-04-19 16:30:37 [environ] CONDA_SHLVL=1
2022-04-19 16:30:37 [environ] SHLVL=2
2022-04-19 16:30:37 [environ] BASH_ENV=/usr/share/modules/init/bash
2022-04-19 16:30:37 [environ] XDG_SESSION_ID=33
2022-04-19 16:30:37 [environ] LD_GOLD=/vol/mbconda/etanis/bin/x86_64-conda-linux-gnu-ld.gold
2022-04-19 16:30:37 [environ] CONDA_PYTHON_EXE=/vol/mbconda/etanis/bin/python
2022-04-19 16:30:37 [environ] XDG_RUNTIME_DIR=/run/user/29280
2022-04-19 16:30:37 [environ] SSH_CLIENT=131.174.27.42 53824 22
2022-04-19 16:30:37 [environ] CONDA_DEFAULT_ENV=base
2022-04-19 16:30:37 [environ] PATH=/scratch/etanis/software/cellranger-6.1.2/lib/bin:/scratch/etanis/software/cellranger-6.1.2/external/martian/bin:/scratch/etanis/software/cellranger-6.1.2/external/anaconda/bin:/scratch/etanis/software/cellranger-6.1.2/bin/tenkit:/scratch/etanis/software/cellranger-6.1.2/bin:/scratch/etanis/software/cellranger-6.1.2:/scratch/etanis/.rstudio/usr/lib/rstudio/bin:/scratch/etanis/software/rstudio/usr/lib/rstudio/bin:/scratch/etanis/.rstudio/usr/lib/rstudio/bin:/scratch/etanis/software/rstudio/usr/lib/rstudio/bin:/vol/mbconda/etanis/bin:/vol/mbconda/etanis/condabin:/usr/local/slurm/bin:/usr/local/openmpi/bin:/usr/local/hwloc/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/cuda/bin:/opt/dell/srvadmin/bin
2022-04-19 16:30:37 [environ] SSH_TTY=/dev/pts/2
2022-04-19 16:30:37 [environ] CONDA_BUILD_SYSROOT=/vol/mbconda/etanis/x86_64-conda-linux-gnu/sysroot
2022-04-19 16:30:37 [environ] BASH_FUNC_ml%%=() {  module ml "$@"
}
2022-04-19 16:30:37 [environ] BASH_FUNC_module%%=() {  _module_raw "$@" 2>&1
}
2022-04-19 16:30:37 [environ] BASH_FUNC__module_raw%%=() {  unset _mlshdbg;
 if [ "${MODULES_SILENT_SHELL_DEBUG:-0}" = '1' ]; then
 case "$-" in 
 *v*x*)
 set +vx;
 _mlshdbg='vx'
 ;;
 *v*)
 set +v;
 _mlshdbg='v'
 ;;
 *x*)
 set +x;
 _mlshdbg='x'
 ;;
 *)
 _mlshdbg=''
 ;;
 esac;
 fi;
 unset _mlre _mlIFS;
 if [ -n "${IFS+x}" ]; then
 _mlIFS=$IFS;
 fi;
 IFS=' ';
 for _mlv in ${MODULES_RUN_QUARANTINE:-};
 do
 if [ "${_mlv}" = "${_mlv##*[!A-Za-z0-9_]}" -a "${_mlv}" = "${_mlv#[0-9]}" ]; then
 if [ -n "`eval 'echo ${'$_mlv'+x}'`" ]; then
 _mlre="${_mlre:-}${_mlv}_modquar='`eval 'echo ${'$_mlv'}'`' ";
 fi;
 _mlrv="MODULES_RUNENV_${_mlv}";
 _mlre="${_mlre:-}${_mlv}='`eval 'echo ${'$_mlrv':-}'`' ";
 fi;
 done;
 if [ -n "${_mlre:-}" ]; then
 eval `eval ${_mlre} /usr/bin/tclsh8.6 /usr/lib/x86_64-linux-gnu/modulecmd.tcl bash '"$@"'`;
 else
 eval `/usr/bin/tclsh8.6 /usr/lib/x86_64-linux-gnu/modulecmd.tcl bash "$@"`;
 fi;
 _mlstatus=$?;
 if [ -n "${_mlIFS+x}" ]; then
 IFS=$_mlIFS;
 else
 unset IFS;
 fi;
 unset _mlre _mlv _mlrv _mlIFS;
 if [ -n "${_mlshdbg:-}" ]; then
 set -$_mlshdbg;
 fi;
 unset _mlshdbg;
 return $_mlstatus
}
2022-04-19 16:30:37 [environ] _=/usr/bin/nice
2022-04-19 16:30:37 [environ] LC_CTYPE=en_US.UTF-8
2022-04-19 16:30:37 [environ] PYTHONNOUSERSITE=1
2022-04-19 16:30:37 [environ] RUST_BACKTRACE=1
2022-04-19 16:30:37 [environ] PYTHONPATH=/scratch/etanis/software/cellranger-6.1.2/external/martian/adapters/python:/scratch/etanis/software/cellranger-6.1.2/lib/python
2022-04-19 16:30:37 [environ] TENX_PRODUCT=cellranger
2022-04-19 16:30:37 [environ] TENX_VERSION=cellranger-6.1.2
2022-04-19 16:30:37 [environ] TENX_COPYRIGHT=Copyright (c) 2021 10x Genomics, Inc.  All rights reserved.
2022-04-19 16:30:37 [environ] MROPATH=/scratch/etanis/software/cellranger-6.1.2/mro
2022-04-19 16:30:37 [version] MRO Version=cellranger-6.1.2
2022-04-19 16:30:37 [options] --jobmode=local
2022-04-19 16:30:37 [options] --vdrmode=rolling
2022-04-19 16:30:37 [options] --profile=disable
2022-04-19 16:30:37 [options] --stackvars=false
2022-04-19 16:30:37 [options] --zip=false
2022-04-19 16:30:37 [options] --limit-loadavg=false
2022-04-19 16:30:37 [options] --noexit=false
2022-04-19 16:30:37 [options] --nopreflight=false
2022-04-19 16:30:37 [jobmngr] Job config = /scratch/etanis/software/cellranger-6.1.2/external/martian/jobmanagers/config.json
2022-04-19 16:30:37 [jobmngr] Using 64 logical cores available on system.
2022-04-19 16:30:37 [jobmngr] Using 906 GB, 90% of system memory.
2022-04-19 16:30:37 [jobmngr] WARNING: configured to use 906GB of local memory, but only 849.5GB is currently available.
2022-04-19 16:30:37 [sysinfo] linux amd64
2022-04-19 16:30:37 [sysinfo] Linux kernel release version: 5.13.0-35-generic
2022-04-19 16:30:37 [sysinfo] glibc version: 2.31
2022-04-19 16:30:37 [filesys] Pipestance path /scratch/etanis/software/cellranger-6.1.2/dimitri_force_10k
2022-04-19 16:30:37 [filesys] Pipestance filesystem type ext
2022-04-19 16:30:37 [filesys] 28 TB and 601,587,805 inodes available.
2022-04-19 16:30:37 [filesys] Pipestance filesystem ext4 mount options: rw,relatime,rw
2022-04-19 16:30:37 [filesys] Bin path /scratch/etanis/software/cellranger-6.1.2/external/martian/bin
2022-04-19 16:30:37 [filesys] Bin filesystem type ext
2022-04-19 16:30:37 [filesys] Bin filesystem ext4 mount options: rw,relatime,rw
Serving UI at http://cn106:35241?auth=BO98I8ISCltqRnlmI2PYca4gdNwwy7UqYdhavL2lN7k

Running preflight checks (please wait)...
2022-04-19 16:30:37 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.REANALYZER_PREFLIGHT
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2022-04-19 16:30:38 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.REANALYZER_PREFLIGHT
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2022-04-19 16:30:38 [runtime] (disabled)        ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.REANALYZE_VERIFY_SAMPLE_IDS
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2022-04-19 16:30:40 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.PREPROCESS_MATRIX
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2022-04-19 16:30:44 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS.fork0.split
2022-04-19 16:30:44 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_FBPCA
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2022-04-19 16:30:44 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_PCA.fork0.split
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2022-04-19 16:30:44 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_PCA
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2022-04-19 16:30:44 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS.fork0.join
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2022-04-19 16:30:47 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION_OUTPUT
2022-04-19 16:30:47 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION_OUTPUT.fork0.chnk0.main
2022-04-19 16:30:47 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.CHOOSE_DIMENSION_REDUCTION_OUTPUT
2022-04-19 16:30:47 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS
2022-04-19 16:30:47 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.split
2022-04-19 16:30:47 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_TSNE
2022-04-19 16:30:47 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_TSNE.fork0.split
2022-04-19 16:30:47 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING
2022-04-19 16:30:47 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING.fork0.split
2022-04-19 16:30:47 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_UMAP
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2022-04-19 16:30:47 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING
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2022-04-19 16:30:47 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_UMAP
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2022-04-19 16:30:47 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_TSNE
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2022-04-19 16:30:48 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS
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2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk1.main
2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk2.main
2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk3.main
2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk4.main
2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk5.main
2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk6.main
2022-04-19 16:30:48 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_KMEANS.fork0.chnk7.main
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2022-04-19 16:30:53 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.COMBINE_CLUSTERING
2022-04-19 16:30:53 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
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2022-04-19 16:30:53 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk0.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk1.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk2.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk3.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk4.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk5.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk6.main
2022-04-19 16:30:53 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.chnk7.main
2022-04-19 16:31:03 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION
2022-04-19 16:31:03 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION.fork0.join
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2022-04-19 16:31:06 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_TSNE
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2022-04-19 16:31:57 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_UMAP
2022-04-19 16:31:57 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.RUN_UMAP.fork0.join
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2022-04-19 16:31:57 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2022-04-19 16:31:57 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork0.split
2022-04-19 16:31:58 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2022-04-19 16:31:58 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork0.chnk0.main
2022-04-19 16:31:58 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS
2022-04-19 16:31:58 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS.fork0.join
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2022-04-19 16:31:59 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SUMMARIZE_REANALYSIS
2022-04-19 16:31:59 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SUMMARIZE_REANALYSIS.fork0.split
2022-04-19 16:31:59 [runtime] (ready)           ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.CLOUPE_PREPROCESS
2022-04-19 16:31:59 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.CLOUPE_PREPROCESS.fork0.split
2022-04-19 16:31:59 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.CLOUPE_PREPROCESS
2022-04-19 16:31:59 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.CLOUPE_PREPROCESS.fork0.chnk0.main
2022-04-19 16:32:00 [runtime] (split_complete)  ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SUMMARIZE_REANALYSIS
2022-04-19 16:32:00 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SUMMARIZE_REANALYSIS.fork0.chnk0.main
2022-04-19 16:32:02 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.SUMMARIZE_REANALYSIS
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2022-04-19 16:32:08 [runtime] (chunks_complete) ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.CLOUPE_PREPROCESS
2022-04-19 16:32:08 [runtime] (run:local)       ID.dimitri_force_10k.SC_RNA_REANALYZER_CS.CLOUPE_PREPROCESS.fork0.join
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2022-04-19 16:32:09 [runtime] VDR killed 211 files, 323 MB.

Outputs:
- Secondary analysis output CSV:          /scratch/etanis/software/cellranger-6.1.2/dimitri_force_10k/outs/analysis
- Secondary analysis web summary:         /scratch/etanis/software/cellranger-6.1.2/dimitri_force_10k/outs/web_summary.html
- Copy of the input parameter CSV:        null
- Copy of the input aggregation CSV:      null
- Loupe Browser file:                     /scratch/etanis/software/cellranger-6.1.2/dimitri_force_10k/outs/cloupe.cloupe
- Filtered feature-barcode matrices MEX:  /scratch/etanis/software/cellranger-6.1.2/dimitri_force_10k/outs/filtered_feature_bc_matrix
- Filtered feature-barcode matrices HDF5: /scratch/etanis/software/cellranger-6.1.2/dimitri_force_10k/outs/filtered_feature_bc_matrix.h5

2022-04-19 16:32:09 [perform] Serializing pipestance performance data.
Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!

2022-04-19 16:32:15 Shutting down.
2022-04-19 16:32:15 [jobmngr] Highest memory usage observed: {
  "rss": 1746108416,
  "shared": 571695104,
  "vmem": 42205323264,
  "text": 221798400,
  "stack": 4266807296,
  "proc_count": 552
}
