This thread is the designated place to ask questions about running the pcawg-bwa-mem-aligner workflow.
Created by James Eddy jaeddy Hi all!
This workflow fails on macOS 10.12.6, cwltool==1.0.20170217172322
When running container `quay.io/pancancer/pcawg-bwa-mem-workflow:2.6.8_1.2`
cwltool sets `--workdir` to `/var/spool/cwl`, which on macOS is resolved to `/private/var/spool/cwl`, because `var -> private/var`, so the working directory is set to `--workdir=/private/var/spool/cwl`. Tool expects working directory to be set to `--workdir=/var/spool/cwl`
Containerized tool fails on
```
+ gosu root chmod a+wrx /var/spool/cwl
chmod: cannot access `/var/spool/cwl': No such file or directory
``` Hi @vipin
It is a similar issue. You can use the docker image `images.sbgenomics.com/bogdang/pcawg-bwa:2.0` for running with `rabix` and on `CGC`. This should get the workflow completed.
Hi,
I tried to run the workflow `pcawg-bwa-mem-aligner` using `rabix` platform. It ends up with the following error message:
```shell
~/rabix-cli-1.0.1/rabix --tmpdir-prefix /home/wfrunner/tmp/ pcawg-bwa-mem-aligner.cwl pcawg-bwa-mem-aligner.json
[2017-12-14 09:19:21.270] [INFO] Job root has started
[2017-12-14 09:20:09.222] [INFO] Pulling docker image quay.io/pancancer/pcawg-bwa-mem-workflow:2.6.8_1.2
[2017-12-14 09:20:10.190] [INFO] Running command line: /start.sh python /home/seqware/Seqware-BWA-Workflow/run_seqware_workflow.py --files /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/hg19.chr22.5x.normal.bam /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/hg19.chr22.5x.normal2.bam --reference-gz /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz --reference-gz-fai /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz.fai --reference-gz-amb /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz.64.amb --reference-gz-ann /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz.64.ann --reference-gz-bwt /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz.64.bwt --reference-gz-pac /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz.64.pac --reference-gz-sa /home/wfrunner/dream_challenge/2017/workflow_execution/workflows/pcawg-bwa-mem-aligner_rabix/input/genome.fa.gz.64.sa --output-dir datastore --output-file-basename hg19.chr22.5x.normal --download-reference-files true
[2017-12-14 09:20:15.237] [ERROR] Job d1e06e0b-2545-4e1f-ac0c-cc41fccb19db failed with exit code 1.
[2017-12-14 09:20:15.240] [INFO] Job d1e06e0b-2545-4e1f-ac0c-cc41fccb19db failed with exit code 1.
[2017-12-14 09:20:15.313] [WARN] Root job d1e06e0b-2545-4e1f-ac0c-cc41fccb19db failed.
[2017-12-14 09:20:16.006] [INFO] Failed to execute a Job
```
Is this something related the issue pointed out in `pcawg-delly-sv-caller` workflow?
Thanks!
Vipin
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