proteomicsLFQ failing with a "correct" SDRF

[ypriverol]

Description of the bug

@jpfeuffer @daichengxin :

ProteomicsLFQ is failing with this SDRF: https://github.com/multiomics/multiomics-configs/blob/master/projects/additional-reanalyses/PXD007145/PXD007145.sdrf.tsv for me it looks OK, but Im getting the following error:

  ProteomicsLFQ \
      -threads 12 \
      -in 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_5.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_1.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_6.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_2.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_1.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_5.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_6.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_4.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_6.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_3.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_4.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_2.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_5.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_3.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_2.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_4.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_3.mzML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_1.mzML \
      -ids 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_5_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_1_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_6_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_2_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_1_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_5_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_6_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_4_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_6_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_3_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_4_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_2_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_5_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_3_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_2_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_4_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_3_comet_feat_perc_pep_filter.idXML 20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_1_comet_feat_perc_pep_filter.idXML \
      -design PXD007145.sdrf_openms_design.tsv \
      -fasta uniprot_yeast_human_rerviewed_decoy.fasta \
      -protein_inference aggregation \
      -quantification_method feature_intensity \
      -targeted_only false \
      -mass_recalibration false \
      -transfer_ids false \
      -protein_quantification unique_peptides \
      -alignment_order star \
      -PeptideQuantification:quantify_decoys \
      -psmFDR 0.01 \
      -proteinFDR 0.01 \
      -picked_proteinFDR true \
      -out_cxml PXD007145.sdrf_openms_design_openms.consensusXML \
      -out PXD007145.sdrf_openms_design_openms.mzTab \
      -out_msstats PXD007145.sdrf_openms_design_msstats_in.csv \
      -out_triqler PXD007145.sdrf_openms_design_triqler_in.tsv \
      -debug 0 \
      |& tee proteomicslfq.log

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ":
      ProteomicsLFQ: $(ProteomicsLFQ 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -c 1-50)
  END_VERSIONS

Command exit status:
  8

Command output:
  Error: Unexpected internal error ((Fraction Group, Fraction, Label) combination can only appear once)

Command wrapper:
  Error: Unexpected internal error ((Fraction Group, Fraction, Label) combination can only appear once)

Work dir:
  /hps/nobackup/juan/pride/reanalysis/quantms-benchmark/PXD007145/work/6d/bd66795d4fad6a518c04a8b91b35d4

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

This is how it looks the openms config:

Fraction_Group  Fraction    Spectra_Filepath    Label   Sample
1   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_1.mzML    1   1
2   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_4.mzML    1   2
3   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_1.mzML   1   3
2   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_2.mzML    1   1
3   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_2.mzML    1   2
4   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_2.mzML   1   3
3   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_3.mzML    1   1
4   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_3.mzML    1   2
5   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_3.mzML   1   3
4   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_1.mzML    1   1
5   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_4.mzML    1   2
6   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_4.mzML   1   3
5   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_5.mzML    1   1
6   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_5.mzML    1   2
7   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_5.mzML   1   3
6   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_1_6.mzML    1   1
7   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_4_6.mzML    1   2
8   1   20171106_LUMOS1_nLC13_AH_TechBench2_LFQ_10_6.mzML   1   3

Sample  MSstats_Condition   MSstats_BioReplicate
1   SP=Yeast;CT=Mixture;QY=1    1
2   SP=Yeast;CT=Mixture;QY=4    2
3   SP=Yeast;CT=Mixture;QY=10   3

Command used and terminal output

No response

Relevant files

No response

System information

No response

[jpfeuffer]

No, the fraction groups must be different for each sample. In this case 1-18

[ypriverol]

We have there different technical replicates, all going from 1-6, and each sample is a biological replicate.

[jpfeuffer]

I know. But does not make a difference. They are all different fraction groups.

[jpfeuffer]

How did you fix it? For future reference.

[ypriverol]

We corrected the biological replicates and the sample names. https://github.com/multiomics/multiomics-configs/blob/master/projects/additional-reanalyses/PXD007145/PXD007145.sdrf.tsv

Im playing today with the tolerances to get more ids.