getfastq --id is currently broken about amalgkit HOT 6 CLOSED

sure!

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yes!
I'm looking into it, but failed to make progress so far. My "fix" created a host of other problems, but I hope I can get a working update out soon.

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@takaW496 Problem should be fixed now. I've also included a --id_list functionality, which can process multiple SRA runs, while --id is reserved for a single run.

--id_list needs a path to a simple text file, where each ID is in a different row.
--id_list does currently only queue the download of each run, but doesn't download them in parallel (this is what I'm looking into next)

I'll close this for now, but feel free to reopen this issue if you encounter any other problems regarding this.

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That sounds the right solution. Could you fix it?

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I got the same error message when I tried to run getfastq process using bioproject ID in gfe pipeline:

Traceback (most recent call last):
  File "/opt/conda/envs/biotools/bin/amalgkit", line 254, in <module>
    args.handler(args)
  File "/opt/conda/envs/biotools/bin/amalgkit", line 31, in command_getfastq
    getfastq_main(args)
  File "/opt/conda/envs/biotools/lib/python3.7/site-packages/amalgkit/getfastq.py", line 517, in getfastq_main
    metadata = getfastq_metadata(args)
  File "/opt/conda/envs/biotools/lib/python3.7/site-packages/amalgkit/getfastq.py", line 477, in getfastq_metadata
    search_term = getfastq_search_term(sra_id, args.entrez_additional_search_term)
NameError: name 'sra_id' is not defined

@Hego-CCTB did you fix the problem? Could you share the fixed script?

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@Hego-CCTB Are you aware of Taka's question?

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