Issue while running on data

[hb660]

Hi,

I think this issue may have already been resolved but I cannot find what is exactly wrong with this run. I already have had several issues I succeeded to fix with previous reported issues but cannot find what's really wrong now ... Can you help me ? cwltool.log

The test on MG37 runs fine, but with the same issue of open files < 8000... I run the ulimit -n 8192 command and now ulimit is on "unlimited" but still have this comment showing up

Thanks a lot in advance Helene

[azat-badretdin]

Thank you, Helene, for your report!

The cwltool.log says:

yaml.parser.ParserError: while parsing a block mapping
  in "<unicode string>", line 1, column 1:
    organism:
    ^
expected <block end>, but found '<block mapping start>'
  in "<unicode string>", line 8, column 2:
     authors:
     ^

It looks like something happened to your input YAML file (submol.yaml).

[hb660]

Thank you for your very fast answer !

I think I fixed it ? I copied/pasted a file I primarly made from the example on the Wiki that uses "-" in front of "author'. I removed it and I think the new issue is not from that ?

Sorry to take up your time again but I think you will point out the issue much faster than me... ( and I am to my 30st try at least so starting to give up a bit..). My submol file is very light for now (hope that's not the issue ?) as I just want it to run and I will do it more properly with all of the information once it finally runs.

Thanks a lot, Helene

cwltool.log

[azat-badretdin]

Could you please post here as attachment your submol YAML file (you can rename it to have .txt if github gives you hard time)?

[hb660]

There. I kept it to the strict minimum but may have chopped too much ? pgap_submol.txt

Edit : I tried to run it with only the "Organism" information in the submol file and it seems to run much better (still running (started 15 min ago). Will see if it works now ... but anyway could you please spot the mistakes I made in the file attached above ? So I can fix it in the future as I will have to submit the sequences at some point so will need to annotate with this information I guess ..

Thanks a lot. Helene

[azat-badretdin]

Thank you for sharing your submol file, Helene.

the "authors: " line should start from the first position in the line, not the second. Please also restore dashes before each "author:"

[hb660]

Ok thanks a lot for your help and your reactivity, I take the liberty to close this issue as my case is resolved.

Helene