gmgitx

###example_sbatch.err
slurmstepd-midway2-0002: error: task/cgroup: unable to add task[pid=14585] to memory cg '(null)'
slurmstepd-midway2-0002: error: Job 50098285 exceeded memory limit (1062800 > 327680), being killed
slurmstepd-midway2-0002: error: Exceeded job memory limit
slurmstepd-midway2-0002: error: *** JOB 50098285 ON midway2-0002 CANCELLED AT 2018-09-25T13:20:08 ***


###example_sbatch.out
[2018-09-25 18:19:47,44] [info] Running with database db.url = jdbc:hsqldb:mem:47a741e8-0324-4c29-a170-f4dd54d61b24;shutdown=false;hsqldb.tx=mvcc
[2018-09-25 18:19:55,46] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000

gmgitx

```sbatch --mem=8g --partition=broadwl run_atac.sh```

```
[2018-09-21 20:02:15,33] [info] Running with database db.url = jdbc:hsqldb:mem:d3447b12-159a-4e42-84ed-95008b9b4607;shutdown=false;hsqldb.tx=mvcc
[2018-09-21 20:02:35,30] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-09-21 20:02:35,33] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-09-21 20:02:35,80] [info] Running with database db.url = jdbc:hsqldb:mem:f9c12bea-bc1b-4b04-9c39-4a44d4e12b5b;shutdown=false;hsqldb.tx=mvcc
[2018-09-21 20:02:36,59] [ESC[38;5;220mwarnESC[0m] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.Pipel$nesApiLifecycleActorFactory for PAPI v2
[2018-09-21 20:02:36,65] [ESC[38;5;220mwarnESC[0m] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-09-21 20:02:36,66] [info] Using noop to send events.

gmgitx

```
tar zxvf debug_issue_31.tar.gz
./test/test_task/ref_output/test_xcor/se/subsample/ENCFF439VSY.subsampled.400.trim.merged.nodup.tn5.no_chrM.5K.cc.qc
./test/test_task/ref_output/test_xcor/pe/subsample/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.no_chrM.R1.5K.cc.qc
./cromwell-executions/atac/5d7e30ce-d8eb-4658-a63c-4972a2b64eff/call-read_genome_tsv/execution/script
./cromwell-executions/atac/5d7e30ce-d8eb-4658-a63c-4972a2b64eff/call-read_genome_tsv/execution/stdout
./cromwell-executions/atac/5d7e30ce-d8eb-4658-a63c-4972a2b64eff/call-read_genome_tsv/execution/stderr
./cromwell-executions/atac/2a0d0464-f14a-4c4d-a994-cf084e712a66/call-read_genome_tsv/execution/script
./cromwell-executions/atac/22b7290b-b6b3-444f-aece-b9d0d367821b/call-read_genome_tsv/execution/script
./cromwell-executions/atac/22b7290b-b6b3-444f-aece-b9d0d367821b/call-read_genome_tsv/execution/stdout

gmgitx

```
    "atac.pipeline_type" : "atac",
    "atac.genome_tsv" : "/project2/name1/name2/DLDS/process_data/hg19db/hg19.tsv",
    "atac.fastqs" : [
        [
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz"],
            ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz",
             "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz"]
        ],

gmgitx

```
[2018-09-19 02:34:46,62] [info] Running with database db.url = jdbc:hsqldb:mem:5c60b7f9-5aef-406c-9ad2-9ff13776de58;shutdown=false;hsqldb.tx=mvcc
[2018-09-19 02:35:04,66] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-09-19 02:35:04,69] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-09-19 02:35:05,18] [info] Running with database db.url = jdbc:hsqldb:mem:2dbdec8e-bc18-4085-b951-aaf4371a1be5;shutdown=false;hsqldb.tx=mvcc
[2018-09-19 02:35:05,81] [warn] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory for PAPI v2
[2018-09-19 02:35:05,86] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-09-19 02:35:05,87] [info] Using noop to send events.
[2018-09-19 02:35:06,19] [info] Slf4jLogger started
[2018-09-19 02:35:06,4

gmgitx

```
2018-09-18 18:03:43,21] [info] Running with database db.url = jdbc:hsqldb:mem:e078c69a-b3bb-476a-8db4-e044a24937ad;shutdown=false;hsqldb.tx=mvcc
[2018-09-18 18:03:58,94] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-09-18 18:03:58,97] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-09-18 18:03:59,30] [info] Running with database db.url = jdbc:hsqldb:mem:2dce6461-a9ba-47df-99b5-72b159e2a478;shutdown=false;hsqldb.tx=mvcc
[2018-09-18 18:03:59,76] [warn] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory for PAPI v2
[2018-09-18 18:03:59,81] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-09-18 18:03:59,82] [info] Using noop to send events.
[2018-09-18 18:04:00,12] [info] Slf4jLogger started
[2018-09-18 18:04:00,36

gmgitx

1. Clone your fork:

git clone git@github.com:YOUR-USERNAME/YOUR-FORKED-REPO.git

2. Add remote from original repository in your forked repository:

cd into/cloned/fork-repo
git remote add upstream git://github.com/ORIGINAL-DEV-USERNAME/REPO-YOU-FORKED-FROM.git
git fetch upstream

gmgitx

#!/bin/bash

# Script for installing tmux on systems where you don't have root access.
# tmux will be installed in $HOME/local/bin.
# It's assumed that wget and a C/C++ compiler are installed.

# exit on error
set -e

TMUX_VERSION=1.8