Hi all. I have previously run this pipeline many t...
# fetchngs
d
Hi all. I have previously run this pipeline many times with no issue, but jsut today it has begun failing on the very first step.
NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO
I cannot get the test case to run
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nextflow run nf-core/fetchngs -profile docker,test --outdir results
results in the error message:
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ERROR ~ Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)` terminated with an error exit status (1)


Command executed:

  echo DRR026872 > id.txt
  sra_ids_to_runinfo.py \
      id.txt \
      DRR026872.runinfo.tsv \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/ubuntu/.nextflow/assets/nf-core/fetchngs/bin/sra_ids_to_runinfo.py", line 498, in <module>
      sys.exit(main())
    File "/home/ubuntu/.nextflow/assets/nf-core/fetchngs/bin/sra_ids_to_runinfo.py", line 491, in main
      valid_vals=get_ena_fields(),
    File "/home/ubuntu/.nextflow/assets/nf-core/fetchngs/bin/sra_ids_to_runinfo.py", line 445, in get_ena_fields
      return [
    File "/home/ubuntu/.nextflow/assets/nf-core/fetchngs/bin/sra_ids_to_runinfo.py", line 446, in <listcomp>
      row["columnId"]
  KeyError: 'columnId'
Really pretty stumped here as nothing has changed about my set up and I've never encountered this problem before. Has anyone run into the same issue?
u
I have the same issue. I suspect something in the ENA response changed