David Tatarakis
03/03/2025, 2:47 PMNFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO
I cannot get the test case to run
nextflow run nf-core/fetchngs -profile docker,test --outdir results
results in the error message:
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?Uri Kleiner
03/04/2025, 8:51 AM