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

delete 52_NGSEPDC_aggr/

parent 9e27da33
{
"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",
"pid": 46872,
"host": "hilbert24",
"type": "pbspro-bmfz",
"cwd": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/split-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": {
"self": {
"ru_maxrss": 3112,
"ru_ixrss": 0,
"ru_idrss": 0,
"ru_minflt": 967,
"ru_majflt": 0,
"ru_nswap": 0,
"ru_utime": 0.001065,
"ru_stime": 0.005325,
"ru_inblock": 0,
"ru_oublock": 0,
"ru_msgsnd": 0,
"ru_msgrcv": 0,
"ru_nsignals": 0
},
"children": {
"ru_maxrss": 98576,
"ru_ixrss": 0,
"ru_idrss": 0,
"ru_minflt": 74373,
"ru_majflt": 0,
"ru_nswap": 0,
"ru_utime": 2.455481,
"ru_stime": 0.513105,
"ru_inblock": 0,
"ru_oublock": 0,
"ru_msgsnd": 0,
"ru_msgrcv": 0,
"ru_nsignals": 0
}
},
"used_bytes": {
"rss": 46927872,
"shared": 17219584,
"vmem": 614944768,
"text": 1716224,
"stack": 275402752,
"proc_count": 1
},
"io": {
"total": {
"read": {
"sysc": 1309,
"bytes": 0
},
"write": {
"sysc": 23,
"bytes": 0
}
},
"max": {
"read": {
"sysc": 348.0926754977392,
"bytes": 0
},
"write": {
"sysc": 4.599716276620852,
"bytes": 0
}
},
"dev": {
"read": {
"sysc": 5.120198057411411,
"bytes": 0
},
"write": {
"sysc": 0.26913261361298496,
"bytes": 0
}
}
},
"wallclock": {
"start": "2019-05-09 10:09:46",
"end": "2019-05-09 10:09:55",
"duration_seconds": 8.918136703
},
"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": "000000002602792E000000005F8C6AA3",
"PBS_JOBDIR": "/home/lautwein",
"PBS_JOBID": "4103642.hpc-batch14",
"PBS_JOBNAME": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CHECK_MOLECULE_INFO_VERSION.fork0.split",
"PBS_MOMPORT": "15003",
"PBS_NODEFILE": "/var/spool/pbs/aux/4103642.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.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/CHECK_MOLECULE_INFO_VERSION/fork0/split-u2265d3e045/_stdout
#PBS -e /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/split-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/split-u2265d3e045/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/split-u2265d3e045/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 \
split \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/split-u2265d3e045 \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CHECK_MOLECULE_INFO_VERSION/fork0/split-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
{
"chunks": [
{
"sample_def": {
"library_id": "Mi1_EPDC",
"molecule_h5": "/scratch_gs/lautwein/cellranger_count/52_NGS_MI1_EPDC/outs/molecule_info.h5"
},
"__mem_gb": 1,
"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,
"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"
},
"__mem_gb": 1,
"mol_h5_version": 3
}
],
"join": {
"__mem_gb": 3
}
}
\ No newline at end of file
@include "_cloupe_stages.mro"
call CLOUPE_PREPROCESS(
pipestance_type = "SC_RNA_AGGREGATOR_CS",
sample_id = "52_NGS_EPDC_aggr",
sample_desc = "",
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",
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",
aggregation_csv = "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/PARSE_CSV/fork0/chnk0-u2265d3e03c/files/aggregation_csv.csv",
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",
no_secondary_analysis = true,
)
\ No newline at end of file
{
"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",
"output_for_cloupe": null
}
\ No newline at end of file
{
"count": 0,
"size": 0,
"timestamp": "2019-05-09 10:32:51",
"paths": null,
"errors": null,
"events": [
{
"Timestamp": "2019-05-09T10:32:26+02:00",
"DeltaBytes": 6734
},
{
"Timestamp": "2019-05-09T10:32:36+02:00",
"DeltaBytes": 6942
},
{
"Timestamp": "2019-05-09T10:32:46+02:00",
"DeltaBytes": 7120
}
]
}
\ No newline at end of file
{
"__mem_gb": 3,
"__threads": 1,
"__vmem_gb": 6,
"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.chnk0",
"pid": 95631,
"host": "hilbert24",
"type": "pbspro-bmfz",
"cwd": "/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1/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": {
"ru_maxrss": 3120,
"ru_ixrss": 0,
"ru_idrss": 0,
"ru_minflt": 965,
"ru_majflt": 0,
"ru_nswap": 0,
"ru_utime": 0.000461,
"ru_stime": 0.005303,
"ru_inblock": 0,
"ru_oublock": 0,
"ru_msgsnd": 0,
"ru_msgrcv": 0,
"ru_nsignals": 0
},
"children": {
"ru_maxrss": 90300,
"ru_ixrss": 0,
"ru_idrss": 0,
"ru_minflt": 69673,
"ru_majflt": 0,
"ru_nswap": 0,
"ru_utime": 2.026607,
"ru_stime": 0.411729,
"ru_inblock": 0,
"ru_oublock": 0,
"ru_msgsnd": 0,
"ru_msgrcv": 0,
"ru_nsignals": 0
}
},
"used_bytes": {
"rss": 2953216,
"shared": 2056192,
"vmem": 261152768,
"text": 1716224,
"stack": 250933248,
"proc_count": 1
},
"io": {
"total": {
"read": {
"sysc": 6,
"bytes": 0
},
"write": {
"sysc": 0,
"bytes": 0
}
},
"max": {
"read": {
"sysc": 295.0742662584937,
"bytes": 0
},
"write": {
"sysc": 0,
"bytes": 0
}
},
"dev": {
"read": {
"sysc": 0,
"bytes": 0
},
"write": {
"sysc": 0,
"bytes": 0
}
}
},
"wallclock": {
"start": "2019-05-09 10:32:36",
"end": "2019-05-09 10:32:40",
"duration_seconds": 3.91821342
},
"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": "000000002C8993FC000000003F15D710",
"PBS_JOBDIR": "/home/lautwein",
"PBS_JOBID": "4103781.hpc-batch14",
"PBS_JOBNAME": "ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.chnk0.main",
"PBS_MOMPORT": "15003",
"PBS_NODEFILE": "/var/spool/pbs/aux/4103781.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.chnk0.main
#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/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1/_stdout
#PBS -e /gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1/_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/chnk0-u2265d3e5a1/files
NUMEXPR_NUM_THREADS=1 \
OMP_NUM_THREADS=1 \
TMPDIR=/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1/tmp \
GOMAXPROCS=1 \
MKL_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 \
main \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1 \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/SC_RNA_AGGREGATOR_CS/CLOUPE_PREPROCESS/fork0/chnk0-u2265d3e5a1/files \
/gpfs/scratch/lautwein/52_NGS_EPDC_aggr/journal/ID.52_NGS_EPDC_aggr.SC_RNA_AGGREGATOR_CS.CLOUPE_PREPROCESS.fork0.chnk0.u2265d3e5a1
2019-05-09 10:32:36 [time] __start__
2019-05-09 10:32:40 [info] Skipping .cloupe generation by instruction (--no-secondary-analysis)
2019-05-09 10:32:40 [time] __end__
{
"output_for_cloupe": null,
"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"
}
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment