ypriverol
commented
1 year ago Even with more memory, it continues failing:
Error executing process > 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER'
Caused by:
Process `NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER` terminated with an error exit status (139)
Command executed:
ProteinInference \
-in ID_mapper_merge.consensusXML \
-threads 48 \
-picked_fdr true \
-picked_decoy_string DECOY_ \
-protein_fdr true \
-Algorithm:use_shared_peptides true \
-Algorithm:annotate_indistinguishable_groups true \
\
-Algorithm:score_aggregation_method best \
-Algorithm:min_peptides_per_protein 1 \
-out ID_mapper_merge_epi.consensusXML \
-debug 0 \
|& tee ID_mapper_merge_inference.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER":
ProteinInference: $(ProteinInference 2>&1 | grep -E '^Version(.*) ' | sed 's/Version: //g' | cut -d ' ' -f 1)
END_VERSIONS
Command exit status:
139
Command output:
Loading input...
Loading input took 41.83 s (wall), 41.62 s (CPU), 0.76 s (system), 40.86 s (user)
<Loading input...> occurred 2 times
Merging IDs across runs...
Merging IDs across runs took 0.00 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user)
Aggregating protein scores...
Building graph on 738370 features, 18751 unassigned spectra (if chosen) and 22415 proteins.
Progress of 'Building graph...':
9.92 %
-- done [took 0.59 s (CPU), 0.60 s (Wall)] --
Progress of 'Annotating indistinguishable proteins...':
-- done [took 2.60 s (CPU), 0.11 s (Wall)] --
Found 17785 connected components.
Aggregating protein scores took 0.00 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user)
Calculating target-decoy q-values...
Storing output...
ConsensusXMLFile::store(): found 1 invalid unique ids
Command error:
.command.sh: line 15: 2292302 Segmentation fault (core dumped) ProteinInference -in ID_mapper_merge.consensusXML -threads 48 -picked_fdr true -picked_decoy_string DECOY_ -protein_fdr true -Algorithm:use_shared_peptides true -Algorithm:annotate_indistinguishable_groups true -Algorithm:score_aggregation_method best -Algorithm:min_peptides_per_protein 1 -out ID_mapper_merge_epi.consensusXML -debug 0 2>&1
2292303 Done | tee ID_mapper_merge_inference.log
Work dir:
/hps/nobackup/juan/pride/reanalysis/differential-expression/tmt/PXD012574/work/b7/2d34857a791de24ebf9f93e632526e
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
jpfeuffer
Description of the bug
URL of the working file: http://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/proteogenomics/benchmakrs/15acadc82868c799e567dd1b219b44/
Command used and terminal output
No response
Relevant files
No response
System information
No response