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

delete 52_NGSEPDC_aggr/

parent 9e27da33
{
"updated_sample_def": {
"library_id": "Mi2_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI2_EPDC/outs/molecule_info.h5"
},
"updated_sample_defs": null
}
\ No newline at end of file
{
"__mem_gb": 1,
"__threads": 1,
"__vmem_gb": 4,
"mol_h5_version": 3,
"sample_def": {
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
},
"sample_defs": [
{
"library_id": "Mi1_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI1_EPDC/outs/molecule_info.h5"
},
{
"library_id": "Mi2_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI2_EPDC/outs/molecule_info.h5"
},
{
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
}
]
}
\ No newline at end of file
{
"name": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0.chnk2",
"pid": 47505,
"host": "hilbert24",
"type": "pbspro-bmfz",
"cwd": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054/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 10:10:02",
"end": "2019-05-09 10:10:07",
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},
"threads": 1,
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"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": "000000003F0D1B8F0000000049CB1B37",
"PBS_JOBDIR": "/home/lautwein",
"PBS_JOBID": "4103645.hpc-batch14",
"PBS_JOBNAME": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0.chnk2.main",
"PBS_MOMPORT": "15003",
"PBS_NODEFILE": "/var/spool/pbs/aux/4103645.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.CHECK_MOLECULE_INFO_VERSION.fork0.chnk2.main
#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/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054/_stdout
#PBS -e /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054/_stderr
#PBS -A HiSeq3000
module load CellRanger/3.0.2
cd /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054/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/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054/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/aggregator/check_molecule_info_version \
main \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054 \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/chnk2-u2265d3e054/files \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/journal/ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0.chnk2.u2265d3e054
{
"updated_sample_def": {
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
},
"updated_sample_defs": null
}
\ No newline at end of file
{
"__mem_gb": 3,
"__threads": 1,
"__vmem_gb": 6,
"sample_defs": [
{
"library_id": "Mi1_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI1_EPDC/outs/molecule_info.h5"
},
{
"library_id": "Mi2_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI2_EPDC/outs/molecule_info.h5"
},
{
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
}
]
}
\ No newline at end of file
[
{
"__mem_gb": 1,
"__threads": 1,
"__vmem_gb": 4,
"mol_h5_version": 3,
"sample_def": {
"library_id": "Mi1_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI1_EPDC/outs/molecule_info.h5"
}
},
{
"__mem_gb": 1,
"__threads": 1,
"__vmem_gb": 4,
"mol_h5_version": 3,
"sample_def": {
"library_id": "Mi2_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI2_EPDC/outs/molecule_info.h5"
}
},
{
"__mem_gb": 1,
"__threads": 1,
"__vmem_gb": 4,
"mol_h5_version": 3,
"sample_def": {
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
}
}
]
\ No newline at end of file
[
{
"updated_sample_def": {
"library_id": "Mi1_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI1_EPDC/outs/molecule_info.h5"
},
"updated_sample_defs": null
},
{
"updated_sample_def": {
"library_id": "Mi2_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI2_EPDC/outs/molecule_info.h5"
},
"updated_sample_defs": null
},
{
"updated_sample_def": {
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
},
"updated_sample_defs": null
}
]
\ No newline at end of file
{
"name": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0",
"pid": 47855,
"host": "hilbert24",
"type": "pbspro-bmfz",
"cwd": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045/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": {
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},
"used_bytes": {
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"shared": 2052096,
"vmem": 261152768,
"text": 1716224,
"stack": 250933248,
"proc_count": 1
},
"io": {
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},
"dev": {
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}
}
},
"wallclock": {
"start": "2019-05-09 10:10:12",
"end": "2019-05-09 10:10:17",
"duration_seconds": 4.610514699
},
"threads": 1,
"memGB": 3,
"vmemGB": 6,
"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": "000000006046D9FD000000003B0BCECE",
"PBS_JOBDIR": "/home/lautwein",
"PBS_JOBID": "4103647.hpc-batch14",
"PBS_JOBNAME": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0.join",
"PBS_MOMPORT": "15003",
"PBS_NODEFILE": "/var/spool/pbs/aux/4103647.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.CHECK_MOLECULE_INFO_VERSION.fork0.join
#PBS -V
#PBS -l select=1:ncpus=1:mem=6gb
#PBS -l walltime=24:00:00
#PBS -o /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045/_stdout
#PBS -e /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045/_stderr
#PBS -A HiSeq3000
module load CellRanger/3.0.2
cd /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045/files
MKL_NUM_THREADS=1 \
NUMEXPR_NUM_THREADS=1 \
OMP_NUM_THREADS=1 \
TMPDIR=/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045/tmp \
GOMAXPROCS=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/aggregator/check_molecule_info_version \
join \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045 \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/join-u2265d3e045/files \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/journal/ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0.u2265d3e045
{
"updated_sample_defs": [
{
"library_id": "Mi1_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI1_EPDC/outs/molecule_info.h5"
},
{
"library_id": "Mi2_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI2_EPDC/outs/molecule_info.h5"
},
{
"library_id": "Mi3_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI3_EPDC/outs/molecule_info.h5"
}
]
}
\ No newline at end of file
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