Commit 4aeba469 authored by Jonas Weber's avatar Jonas Weber
Browse files

delete 52_NGSEPDC_aggr/

parent 9e27da33
{
"__mem_gb": 1,
"__threads": 1,
"__vmem_gb": 4,
"aggregation_csv": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/PARSE_CSV/fork0/chnk0-u2265d3e03c/files/aggregation_csv.csv",
"analysis": null,
"filtered_gene_bc_matrices_h5": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/SC_RNA_AGGREGATOR/WRITE_MATRICES/fork0/join-u2265d3e1ee/files/filtered_matrix_h5.h5",
"gem_group_index_json": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/SC_RNA_AGGREGATOR/SETUP_SAMPLES/fork0/chnk0-u2265d3e075/files/gem_group_index_json.json",
"metrics_json": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/SC_RNA_AGGREGATOR/SUMMARIZE_AGGREGATED_REPORTS/fork0/join-u2265d3e571/files/summary.json",
"no_secondary_analysis": true,
"pipestance_type": "SC_RNA_AGGREGATOR_CS",
"sample_desc": "",
"sample_id": "52_NGS_EPDC_aggr"
}
\ No newline at end of file
[
{
"__mem_gb": 3,
"__threads": 1,
"__vmem_gb": 6
}
]
\ No newline at end of file
[
{
"gem_group_index_json": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1/files/gem_group_index_json.json",
"output_for_cloupe": null
}
]
\ No newline at end of file
{
"name": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0",
"pid": 95857,
"host": "hilbert24",
"type": "pbspro-bmfz",
"cwd": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/files",
"python": {
"binpath": "/software/CellRanger/3.0.2/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/bin/python",
"version": "2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 17:29:31) \n[GCC 7.2.0]"
},
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"wallclock": {
"start": "2019-05-09 10:32:46",
"end": "2019-05-09 10:32:50",
"duration_seconds": 3.948802529
},
"threads": 1,
"memGB": 1,
"vmemGB": 4,
"profile_mode": "disable",
"stackvars_flag": "disable",
"monitor_flag": "disable",
"invocation": {
"call": "SC_RNA_AGGREGATOR_CS",
"args": {
"aggregation_csv": "/gpfs/scratch/lautwein/cellranger_aggr_EPDC.csv",
"no_secondary_analysis": true,
"normalization_mode": "mapped",
"pipestance_root": "/gpfs/scratch/lautwein",
"sample_desc": "",
"sample_id": "52_NGS_EPDC_aggr"
},
"sweepargs": []
},
"version": {
"martian": "'3.0.2-v3.2.0'",
"pipelines": "3.0.2"
},
"sge": {
"PBS_ACCOUNT": "HiSeq3000",
"PBS_ENVIRONMENT": "PBS_BATCH",
"PBS_JOBCOOKIE": "000000001551730B000000007DC5B1B0",
"PBS_JOBDIR": "/home/lautwein",
"PBS_JOBID": "4103782.hpc-batch14",
"PBS_JOBNAME": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.join",
"PBS_MOMPORT": "15003",
"PBS_NODEFILE": "/var/spool/pbs/aux/4103782.hpc-batch14",
"PBS_NODENUM": "0",
"PBS_QUEUE": "workq",
"PBS_TASKNUM": "1"
}
}
\ No newline at end of file
#!/usr/bin/env bash
#
# Copyright (c) 2016 10x Genomics, Inc. All rights reserved.
#
# =============================================================================
# Setup Instructions
# =============================================================================
#
# 1. Add any other necessary PBSpro arguments such as queue (-q) or account
# (-A). If your system requires a walltime (-l walltime), 24 hours (24:00:00)
# is sufficient. We recommend you do not remove any arguments below or
# Martian may not run properly.
#
# 2. Change filename of pbspro.template.example to pbspro.template.
#
# =============================================================================
# Template
# =============================================================================
#
#PBS -N ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.join
#PBS -V
#PBS -l select=1:ncpus=1:mem=4gb
#PBS -l walltime=24:00:00
#PBS -o /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/_stdout
#PBS -e /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/_stderr
#PBS -A HiSeq3000
module load CellRanger/3.0.2
cd /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/files
GOMAXPROCS=1 \
MKL_NUM_THREADS=1 \
NUMEXPR_NUM_THREADS=1 \
OMP_NUM_THREADS=1 \
TMPDIR=/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/tmp \
/software/CellRanger/3.0.2/martian-cs/v3.2.0/bin/mrjob \
/software/CellRanger/3.0.2/martian-cs/v3.2.0/adapters/python/martian_shell.py \
/software/CellRanger/3.0.2/cellranger-cs/3.0.2/mro/stages/cloupe/cloupe_preprocess \
join \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595 \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/files \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/journal/ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.u2265d3e595
2019-05-09 10:32:46 [time] __start__
2019-05-09 10:32:50 [time] __end__
{
"output_for_cloupe": null,
"gem_group_index_json": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/join-u2265d3e595/files/gem_group_index_json.json"
}
\ No newline at end of file
{
"aggregation_csv": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/PARSE_CSV/fork0/chnk0-u2265d3e03c/files/aggregation_csv.csv",
"analysis": null,
"filtered_gene_bc_matrices_h5": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/SC_RNA_AGGREGATOR/WRITE_MATRICES/fork0/join-u2265d3e1ee/files/filtered_matrix_h5.h5",
"gem_group_index_json": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/SC_RNA_AGGREGATOR/SETUP_SAMPLES/fork0/chnk0-u2265d3e075/files/gem_group_index_json.json",
"metrics_json": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/SC_RNA_AGGREGATOR/SUMMARIZE_AGGREGATED_REPORTS/fork0/join-u2265d3e571/files/summary.json",
"no_secondary_analysis": true,
"pipestance_type": "SC_RNA_AGGREGATOR_CS",
"sample_desc": "",
"sample_id": "52_NGS_EPDC_aggr"
}
\ No newline at end of file
{
"name": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0",
"pid": 95404,
"host": "hilbert24",
"type": "pbspro-bmfz",
"cwd": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595/files",
"python": {
"binpath": "/software/CellRanger/3.0.2/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/bin/python",
"version": "2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 17:29:31) \n[GCC 7.2.0]"
},
"rusage": {
"self": {
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"ru_ixrss": 0,
"ru_idrss": 0,
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"children": {
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},
"used_bytes": {
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"proc_count": 1
},
"io": {
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}
},
"wallclock": {
"start": "2019-05-09 10:32:26",
"end": "2019-05-09 10:32:30",
"duration_seconds": 3.904738578
},
"threads": 1,
"memGB": 1,
"vmemGB": 4,
"profile_mode": "disable",
"stackvars_flag": "disable",
"monitor_flag": "disable",
"invocation": {
"call": "SC_RNA_AGGREGATOR_CS",
"args": {
"aggregation_csv": "/gpfs/scratch/lautwein/cellranger_aggr_EPDC.csv",
"no_secondary_analysis": true,
"normalization_mode": "mapped",
"pipestance_root": "/gpfs/scratch/lautwein",
"sample_desc": "",
"sample_id": "52_NGS_EPDC_aggr"
},
"sweepargs": []
},
"version": {
"martian": "'3.0.2-v3.2.0'",
"pipelines": "3.0.2"
},
"sge": {
"PBS_ACCOUNT": "HiSeq3000",
"PBS_ENVIRONMENT": "PBS_BATCH",
"PBS_JOBCOOKIE": "00000000202EFA8C0000000038207815",
"PBS_JOBDIR": "/home/lautwein",
"PBS_JOBID": "4103780.hpc-batch14",
"PBS_JOBNAME": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.split",
"PBS_MOMPORT": "15003",
"PBS_NODEFILE": "/var/spool/pbs/aux/4103780.hpc-batch14",
"PBS_NODENUM": "0",
"PBS_QUEUE": "workq",
"PBS_TASKNUM": "1"
}
}
\ No newline at end of file
#!/usr/bin/env bash
#
# Copyright (c) 2016 10x Genomics, Inc. All rights reserved.
#
# =============================================================================
# Setup Instructions
# =============================================================================
#
# 1. Add any other necessary PBSpro arguments such as queue (-q) or account
# (-A). If your system requires a walltime (-l walltime), 24 hours (24:00:00)
# is sufficient. We recommend you do not remove any arguments below or
# Martian may not run properly.
#
# 2. Change filename of pbspro.template.example to pbspro.template.
#
# =============================================================================
# Template
# =============================================================================
#
#PBS -N ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.split
#PBS -V
#PBS -l select=1:ncpus=1:mem=4gb
#PBS -l walltime=24:00:00
#PBS -o /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595/_stdout
#PBS -e /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595/_stderr
#PBS -A HiSeq3000
module load CellRanger/3.0.2
cd /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595/files
OMP_NUM_THREADS=1 \
TMPDIR=/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595/tmp \
GOMAXPROCS=1 \
MKL_NUM_THREADS=1 \
NUMEXPR_NUM_THREADS=1 \
/software/CellRanger/3.0.2/martian-cs/v3.2.0/bin/mrjob \
/software/CellRanger/3.0.2/martian-cs/v3.2.0/adapters/python/martian_shell.py \
/software/CellRanger/3.0.2/cellranger-cs/3.0.2/mro/stages/cloupe/cloupe_preprocess \
split \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595 \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/split-u2265d3e595/files \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/journal/ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.u2265d3e595
2019-05-09 10:32:26 [time] __start__
2019-05-09 10:32:30 [info] Skipping .cloupe generation by instruction (--no-secondary-analysis)
2019-05-09 10:32:30 [time] __end__
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