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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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No identification results #525

Closed fiuzatayna closed 1 year ago

fiuzatayna commented 1 year ago

I'm using the files from this tutorial with the docker images for SearchGUI/CLI and PeptideShaker.

Here is what I did so far:

IdentificationParametersCLI

root@a94c2a0ee089:/myresources# searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -fixed_mods 'Carbamidomethylation of C' -variable_mods 'Oxidation of M' -frag_ppm 0 -frag_tol 0.2 -max_charge 6 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -out /myresources/searchgui_beringstrait_lessStrict.par
Identification parameters file created: /myresources/searchgui_beringstrait_lessStrict.par

SearchCLI

root@a94c2a0ee089:/myresources# searchgui eu.isas.searchgui.cmd.SearchCLI -spectrum_files "/myresources/mgf-files/2016_Jan_12_QE2_45.mgf,/myresources/mgf-files/2016_Jan_12_QE2_46.mgf,/myresources/mgf-files/2016_Jan_12_QE2_47.mgf" -fasta_file "/myresources/fasta/FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta" -output_folder "/myresources/outPut/bering/" -id_params "/myresources/searchgui_beringstrait_lessStrict.par"
Fri Sep 15 18:26:15 GMT 2023 Importing spectrum files.
Fri Sep 15 18:26:15 GMT 2023 Importing spectrum file 2016_Jan_12_QE2_45.mgf
Fri Sep 15 18:26:15 GMT 2023 Importing spectrum file 2016_Jan_12_QE2_46.mgf
Fri Sep 15 18:26:15 GMT 2023 Importing spectrum file 2016_Jan_12_QE2_47.mgf
Fri Sep 15 18:26:15 GMT 2023 Importing spectrum files completed (105.0 milliseconds).

Processing: 2016_Jan_12_QE2_45.mgf (1/3)

Processing: 2016_Jan_12_QE2_46.mgf (2/3)

Processing: 2016_Jan_12_QE2_47.mgf (3/3)

Fri Sep 15 18:26:15 GMT 2023 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Fri Sep 15 18:26:15 GMT 2023 Search Completed (234.0 milliseconds).

Search Completed.

Altough suspiciously quick, no errors or warnings were exhibited. Then I tried:

peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI -reference beringTutorial -fasta_file "/myresources/fasta/FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta" -spectrum_files "/myresources/mgf-files/2016_Jan_12_QE2_45.mgf,/myresources/mgf-files/2016_Jan_12_QE2_46.mgf,/myresources/mgf-files/2016_Jan_12_QE2_47.mgf" -id_params "/myresources/searchgui_beringstrait_lessStrict.par" -identification_files "/myresources/outPut/bering/searchgui_out.zip"
Fri Sep 15 17:58:47 GMT 2023 Unzipping searchgui_out.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Fri Sep 15 17:58:48 GMT 2023 Import process for beringTutorial

Fri Sep 15 17:58:48 GMT 2023 Importing sequences from FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta.
Fri Sep 15 17:58:49 GMT 2023 Importing gene mappings.
Fri Sep 15 17:58:50 GMT 2023 Establishing local database connection.
Fri Sep 15 17:58:50 GMT 2023 Reading identification files.
Fri Sep 15 17:58:50 GMT 2023 No identification results.
Fri Sep 15 17:58:50 GMT 2023 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /usr/local/share/peptide-shaker-2.2.25-0/resources/PeptideShaker.log</CompomicsError

Can you help me see what I'm missing? As far as I can see, I'm using the same parameters as the tutorial.

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PeptideShaker version 2.2.25 from quay.io/biocontainers/peptide-shaker:2.2.25--hdfd78af_0 SearchGUI version 4.2.17 from quay.io/biocontainers/searchgui:4.2.17--hdfd78af_0

hbarsnes commented 1 year ago

You have to tell SearchGUI which search engines to use. For example by adding -xtandem 1 to your SearchCLI command line.

See https://github.com/compomics/searchgui/wiki/SearchCLI#optional-common-parameters for the complete list of supported search engines.

fiuzatayna commented 1 year ago

Oops, I was doing it on a previous run and I forgot to add it this time. Such a simple fix. Thanks a lot, I'll try it soon.

Em sex., 15 de set. de 2023 17:44, Harald Barsnes @.***> escreveu:

You have to tell SearchGUI which search engines to use. For example by adding -xtandem 1 to your SearchCLI command line.

See https://github.com/compomics/searchgui/wiki/SearchCLI#optional-common-parameters for the complete list of supported search engines.

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