ERROR Tool definition failed validation

[nmc-ei]

Hi, I try to create indices.

createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml
　　　　　　　　　　　　　　　　　　　　　　　　　　　OR
createindex.cwl workflow/createindex.job.yaml
　　　　　　　　　　　　　　　　　　　　　　　　　　　OR
cwltool --singularity workflow/createindex.cwl workflow/createindex.job.yaml

but these command return error.

INFO /home/hoge/anaconda3/envs/cwl_env/bin/cwltool 3.1.20210426140515
INFO Resolved '/share/home/hoge/VIRTUS/bin/createindex.cwl' to 'file:///yshare2/home/hoge/VIRTUS/bin/createindex.cwl'
../../../../home/hoge/VIRTUS/bin/createindex.cwl:39:5: object id `../../../../home/hoge/VIRTUS/bin/createindex.cwl#createindex/salmon_index_human` previously defined
../../../../home/hoge/VIRTUS/bin/createindex.cwl:39:5: object id `../../../../home/hoge/VIRTUS/bin/createindex.cwl#createindex/salmon_index_human` previously defined
../../../../home/hoge/VIRTUS/bin/createindex.cwl:148:9: object id `../../../../home/hoge/VIRTUS/bin/createindex.cwl#createindex/salmon_index_human/index` previously defined
ERROR Tool definition failed validation:
../../../../home/hoge/VIRTUS/bin/createindex.cwl:10:1: union[str, int, bool, schema_salad.avro.schema.Schema, list, list, dict, list, None] object expected; got ruamel.yaml.scalarfloat.ScalarFloat

Thank you.

[yyoshiaki]

Hi, thank you for using our tool!

I tried createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml on several machines and environments including cwltool 3.1.20210426140515, but I failed to reproduce the error. Did you edit the cwl files on your computer?

Yoshi

[nmc-ei]

Thank you for your reply.

No. I didn't edit the cwl files.

[yyoshiaki]

What are your Python and schema_salad version? If 3.9, this PR may solve the problem. https://github.com/common-workflow-language/schema_salad/issues/385 https://github.com/common-workflow-language/schema_salad/pull/386

[nmc-ei]

I checked the version of schema_salad and found that it was not installed for some reason, so I reinstalled cwlref-runner. Then the command "cwltool --singularity workflow/createindex.cwl workflow/createindex.job.yaml" was ran without error. However, some warnings are present.

WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
WARNING: Building container as an unprivileged user. If you run this container as root
WARNING: it may be missing some functionality.
WARNING [job wget_transcipt] completed permanentFail
WARNING [step wget_transcipt] completed permanentFail
WARNING Final process status is permanentFail

Can I ignore these warnings?

[yyoshiaki]

WARNING Final process status is permanentFail

It seems the process failed. Can you share the output files?

[nmc-ei]

Do you mean you need all the standard output? virtus_output.txt

[yyoshiaki]

The process looks not to have been appropriately finished. I do not understand how Singularity works well. Can you switch it to docker?

or, /tmp/0uibbzdw/wget-stderr.log may contain information about the solution.

[nmc-ei]

I can't switch it to doker. And I can't found /tmp/0uibbzdw/wget-stderr.log.

[yyoshiaki]

I verified --singularity worked as well on our computer. Can you add --debug flag and execute createindex.cwl again?

[nmc-ei]

virtus_output_debug.txt

[yyoshiaki]

put options before files like

cwltool --debug --singularity workflow/createindex.cwl workflow/createindex.job.yaml

[nmc-ei]

Sorry. virtus_output_debug2.txt

[yyoshiaki]

Thank you. The download of https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/data/viruses.fasta looks succeeded whereas that of ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.transcripts.fa.gz failed. Because both procedures use the same container, it may be due to a fire wall or something. Can you do wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.transcripts.fa.gz on your computer? Otherwise, I have completely no idea...

[nmc-ei]

I try wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.transcripts.fa.gz. But it failed due to errors in the server response.

I apologize for any inconvenience this may cause. Thank you very much.

[yyoshiaki]

It's my pleasure, thank you for trying our tool and reporting an issue!