Closed ashenfernando1 closed 3 months ago
@ashenfernando1 this is because the test profile (-profile test,docker
) doesn't work with the --run_ancestry
command. You'll need to supply actual samples with a samplesheet to try it out https://pgsc-calc.readthedocs.io/en/latest/how-to/samplesheet.html
thanks for the quick reply @smlmbrt. So I had tried with samples and a samplesheet and ran into a different error, so I wanted to see if there was a --run_ancestry
canned example to verify everything was working as intended.
I'll expand a little on the error with the supplied samples and samplesheet, but let me know if it would be more appropriate to create a separate issue/query:
It fails like so:
ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ (testtirtya null afreq)'
Caused by:
Process `PGSCATALOG_PGSCCALC:PGSCCALC:APPLY_SCORE:RELABEL_AFREQ (testtirtya null afreq)` terminated with an error exit status (1)
Command executed:
relabel_ids --maps testtirtya_ALL_matched.txt.gz --col_from ID_REF --col_to ID_TARGET --target_file GRCh37_reference.afreq.zst --target_col ID --dataset testtirtya.afreq --verbose --combined
cat <<-END_VERSIONS > versions.yml
RELABEL_AFREQ:
pgscatalog_utils: $(echo $(python -c 'import pgscatalog_utils; print(pgscatalog_utils.__version__)'))
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
root: 2024-03-31 17:02:06 DEBUG Verbose logging enabled
pgscatalog_utils.relabel.relabel_ids: 2024-03-31 17:02:06 DEBUG Writing combined output enabled
pgscatalog_utils.relabel.relabel_ids: 2024-03-31 17:02:06 DEBUG Reading map file testtirtya_ALL_matched.txt.gz with gzip.open
pgscatalog_utils.relabel.relabel_ids: 2024-03-31 17:02:27 DEBUG Opening testtirtya.afreq_ALL_relabelled.gz and writing header
Traceback (most recent call last):
File "/venv/bin/relabel_ids", line 8, in <module>
sys.exit(relabel_ids())
File "/venv/lib/python3.10/site-packages/pgscatalog_utils/relabel/relabel_ids.py", line 179, in relabel_ids
[_relabel_target(args=args, mapping=mapping, split_output=x) for x in split_output]
File "/venv/lib/python3.10/site-packages/pgscatalog_utils/relabel/relabel_ids.py", line 179, in <listcomp>
[_relabel_target(args=args, mapping=mapping, split_output=x) for x in split_output]
File "/venv/lib/python3.10/site-packages/pgscatalog_utils/relabel/relabel_ids.py", line 104, in _relabel_target
_relabel(in_target=io.TextIOWrapper(reader), mapping=mapping, split_output=split_output, args=args)
File "/venv/lib/python3.10/site-packages/pgscatalog_utils/relabel/relabel_ids.py", line 149, in _relabel
line[i_target_col] = mapping[line[i_target_col]] # revalue column
KeyError: '22:25761309:C:T'
Is this KeyError: '22:25761309:C:T'
particularly informative? The samplesheet chrom column is empty because of multiple chromosomes.
I've only seen this happen when it's started the pipeline from a resume. Delete the work directory and the cache and start again.
Description of the bug
Maybe similar to https://github.com/PGScatalog/pgsc_calc/issues/252, but haven't found a resolution yet.
nextflow run pgscatalog/pgsc_calc -profile test,docker
completes successfully.nextflow run pgscatalog/pgsc_calc -profile test,docker --max_memory 30GB --max_cpus 14 --run_ancestry /procedure/data/local_data/USEFUL_FILES_VCF_/pgsc_HGDP+1kGP_v1.tar.zst
fails, on a user account that correctly runs dockerIf you have any thoughts on what may be going wrong, I would really appreciate it.
Relevant files
nextflow.log
System information
Ubuntu 22.04.01 (Linux VM), nextflow version 23.10.1.5891