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nf-core / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://nf-co.re/quantms
MIT License
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DIA-NN Analysis parameters always trigger DDA-LFQ jobs? #142

Closed J-Burgess closed 5 months ago

J-Burgess commented 7 months ago

Description of the bug

Hi, thanks for the all useful docs and work so far!

I am currently trying to run DIA data through quantms. We are primarily interested in Phosphoproteomics but I would like to run the data through DIA-NN to see how feasible our outputs are for use. From the flowchart in the homepage, it appears that in DIA-LFQ mode the pipeline should not run Comet or percolator and instead go straight into DIA-NN after mzML indexing.

However, with my run the thermorawparser completes successfully and yet ProteomicsLFQ amongst other steps such as Percolator is carried out. It always errors out at the NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ with an error no proteins remaining after FDR message. I am new to proteomics (and Nextflow!) but from the docs I can see that it states the comet search engine and these steps are not appropriate for DIA data? Could this be the cause of the error?

Based on the argument parameters, I do not think my command line is triggering any DDA-LFQ jobs but perhaps it is something in the SDRF? In addition: WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC?

Thanks in advance!

Kind regards, James

Command used and terminal output

nextflow run nf-core/quantms -r 1.2.0 --input '/home/james.burgess/projects/JB240122_MaxQuant_MSQuant_Benchmarking/MaxQuant_MSquant_Linux_Benchmarking/quantms/JB230130_quantms_input.sdrf.tsv' --root_folder '/ibm/hpcfs1/tmp/JB230123_DATA/DATA/raw' --database '/ibm/hpcfs1/tmp/JB230123_DATA/DATA/MaxDIA/fasta/JB230123_quantms_database.fasta' --outdir '/ibm/hpcfs1/tmp/JB230123_DATA/DATA/JB230123_quantms_proc' --acquisition_method 'dia' --max_cpus 60 --max_memory 150GB  -profile singularity -resume

[8e/b7eb83] process > NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (JB230130_quantms_input.sdrf.tsv) [  0%] 0 of 1
[-        ] process > NFCORE_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING                                -
[-        ] process > NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS                                     -
[-        ] process > NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING                                   -
[-        ] process > NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER                            -
[-        ] process > NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS                                 -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES                          -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:PERCOLATOR                                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMFDRCONTROL:IDSCORESWITCHER                            -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMFDRCONTROL:IDFILTER                                   -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:FEATUREMAPPER:ISOBARICANALYZER                              -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:FEATUREMAPPER:IDMAPPER                                      -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:FILEMERGE                                                   -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:PROTEININFERENCER                          -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:IDFILTER                                   -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:IDCONFLICTRESOLVER                             -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:PROTEINQUANTIFIER                              -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:MSSTATSCONVERTER                               -
[-        ] process > NFCORE_QUANTMS:QUANTMS:TMT:MSSTATSTMT                                                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:EXTRACTPSMFEATURES                          -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:PSMRESCORING:PERCOLATOR                                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:PSMFDRCONTROL:IDSCORESWITCHER                            -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:ID:PSMFDRCONTROL:IDFILTER                                   -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ                                               -
[-        ] process > NFCORE_QUANTMS:QUANTMS:LFQ:MSSTATS                                                     -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:DIANNCFG                                                    -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:SILICOLIBRARYGENERATION                                     -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:DIANN_PRELIMINARY_ANALYSIS                                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY                                  -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:INDIVIDUAL_FINAL_ANALYSIS                                   -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:DIANNSUMMARY                                                -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:DIANNCONVERT                                                -
[-        ] process > NFCORE_QUANTMS:QUANTMS:DIA:MSSTATS                                                     -
[-        ] process > NFCORE_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS                                     -
[-        ] process > NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE                                                 -
WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC?

Relevant files

JB230130_quantms_input.txt

System information

Nextflow version: 23.10.1.5891
Hardware: HPC
Executor: local
Container engine: Singularity, Conda
OS: Linux 4.18.0-513.5.1.el8_9.x86_64
Version of nf-core/quantms: 1.2.0
ypriverol commented 5 months ago

In the SDRF you have to specify the Data independent acquisition in the column for acquisition mode.