test error

[mabouelk]

Hi I am so exicted to use your tool and cite it in my paper. Please can you help me? mabouelk@js-17-152:~/VIRTUS/test$ bash test.sh

• [[ ! -e ./ERR3240275/ERR3240275_1.fastq.gz ]]
• mkdir -p ERR3240275
• cd ERR3240275
• echo null
• ls
• grep -v -E ERR3240275_1.fastq.gz
• grep -v -E ERR3240275_2.fastq.gz
• xargs rm -r
• cd ..
• [[ ! -e ./SRR8315715/SRR8315715_1.fastq.gz ]]
• mkdir -p SRR8315715
• cd SRR8315715
• echo null
• ls
• grep -v -E SRR8315715_1.fastq.gz
• grep -v -E SRR8315715_2.fastq.gz
• xargs rm -r
• cd ..
• echo null
• ls
• grep -v -E test.sh
• grep -v -E ERR3240275
• xargs rm -r
• grep -v -E SRR8315715
• ../workflow/createindex.cwl ../workflow/createindex.job.yaml /usr/bin/env: ?cwltool?: No such file or directory

[mabouelk]

ok, I managed to reinstall cwltool using miniconda but I got this error: ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information. The error was: cwltool requires Node.js engine to evaluate and validate Javascript expressions, but couldn't find it. Tried nodejs, node, docker run node:slim

[yyoshiaki]

Hi, @mabouelk, Thank you for trying our tool!

You look failing the installation of cwl. Please refer to https://github.com/common-workflow-language/cwltool .

[mabouelk]

Thank you so much for your quick response, I did but I got this ERROR Workflow or tool uses unsupported feature: Docker is required to run this tool: Command '['docker', 'images', '--no-trunc', '--all']' returned non-zero exit status 1.

[yyoshiaki]

Install Docker!

[mabouelk]

I am using my institution virtual machine which already has docker. I tried to run it on my macbook pro but It failed (i think because the memory is not enough!) :

[job star_index] Max memory used: 14558MiB WARNING [job star_index] completed permanentFail WARNING [step star_index] completed permanentFail INFO [workflow rnaseq_star_index_human] completed permanentFail WARNING [step rnaseq_star_index_human] completed permanentFail INFO [workflow ] completed permanentFail { "downloaded_virus": null, "starIndex_virus": null, "starIndex_human": { "location": "file:///Users/moh/VIRTUS/test/STAR_index_human", "basename": "STAR_index_human", "class": "Directory", "listing": [], "path": "/Users/moh/VIRTUS/test/STAR_index_human" }, "downloaded_genomefasta_human": { "location": "file:///Users/moh/VIRTUS/test/GRCh38.p13.genome.fa.gz", "basename": "GRCh38.p13.genome.fa.gz", "class": "File", "checksum": "sha1$2b7cdbbf55b0c507ad6f56de3afb2fe9ff8a8da5", "size": 889409368, "path": "/Users/moh/VIRTUS/test/GRCh38.p13.genome.fa.gz" }, "salmon_index_human": null, "downloaded": { "location": "file:///Users/moh/VIRTUS/test/gencode.v33.transcripts.fa.gz", "basename": "gencode.v33.transcripts.fa.gz", "class": "File", "checksum": "sha1$a1ea3698bb266dcc05f12524037203f9bdf4da5b", "size": 72861419, "path": "/Users/moh/VIRTUS/test/gencode.v33.transcripts.fa.gz" } } WARNING Final process status is permanentFail

[mabouelk]

back to the cluster, I fixed the installation but it stop and I see that in the log file

ocker: Error response from daemon: invalid mount config for type "bind": \ bind source path does not exist: /tmp/_igilf53. See 'docker run --help'.

[yyoshiaki]

>32Gb RAM is required, so the cluster is better.

about the docker bug, I cannot solve it quickly. Maybe, it is relating to the docker installation and configuration on your cluster. Please make sure whether docker works well besides VIRTUS, the docker version, and related issues on Google.

If I come up with an idea, I share it.

[yyoshiaki]

@mabouelk If it is difficult to install Docker on your cluster, udocker is another option. Good luck!