vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Failed after generating precursor levels matrix #1266

Open yashacode opened 3 hours ago

yashacode commented 3 hours ago

Hello, I am running DIANN on an HPC and it's failing before generating all of the reports. Here is the end of the output file: [281:53] Cross-run analysis [281:53] Reading quantification information: 153 files [283:25] Quantifying peptides [289:06] Assembling protein groups [289:09] Quantifying proteins [289:14] Calculating q-values for protein and gene groups [290:03] Calculating global q-values for protein and gene groups [290:03] Protein groups with global q-value <= 0.01: 19810 [291:05] Compressed report saved to ./virus_neurons.report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process [291:05] Writing report [294:03] Report saved to ./virus_neurons.report-first-pass.tsv. [294:03] Saving precursor levels matrix [294:07] Precursor levels matrix (1% precursor and protein group FDR) saved to ./virus_neurons.report-first-pass.pr_matrix.tsv. [294:07] Manifest saved to ./virus_neurons.report-first-pass.manifest.txt terminate called after throwing an instance of 'std::length_error' what(): basic_string::_M_create /usr/local/apps/diann/1.9.1/bin/diann: line 13: 4040771 Aborted singularity exec --cleanenv "${selfdir}/libexec/${sif_file}" "$cmd" "$@"

This is the config file I used: --fasta human_reviewed_5virus.fasta --dir /data/CARD_challenge/virus_neurons/human_brain_data/insoluble_mzML_files/ --verbose 1 --out ./virus_neurons.report.tsv --qvalue 0.01 --matrices --out-lib ./report-lib.tsv --gen-spec-lib --predictor --fasta-search --min-fr-mz 200 --max-fr-mz 2000 --met-excision --cut K,R --missed-cleavages 2 --min-pep-len 7 --max-pep-len 52 --min-pr-mz 300 --max-pr-mz 1800 --min-pr-charge 1 --max-pr-charge 4 --var-mods 5 --var-mod UniMod:35,15.994915,M --var-mod UniMod:1,42.010565,*n --reanalyse --matrices --smart-profiling --met-excision --relaxed-prot-inf

vdemichev commented 3 hours ago

Hi Jacob,

This is an issue that has been fixed in 1.9.2. In 1.9.1, just need not to use --matrices on Linux.

Best, Vadim