Peptide-shaker doesn't progress from "Importing PSMs from mgf.comet.pep.xml.gz"

[MigRibe]

I'm trying to use the search gui and peptide shaker for peptide mass fingerprinting. Both seem pretty intuitive and complete, but I can't make progress on some algorithms in the search gui, but mostly in the peptide shaker. Attached figure. Could you help me, please?

[hbarsnes]

If PeptideShaker is stuck at that particular step for long, you can cancel the process and have a look at the PeptideShaker log file. You can find it from the PeptideShaker Welcome dialog > Settings & Help > Help > Bug Report. If you share that file here we can hopefully figure out what is going on.

[MigRibe]

Yes, PeptideShaker is stuck at “Importing PSMs from glutenmgf.comet.pep.xml.gz”. Bug log in appendix. Many thanks Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows De: Harald ***@***.***> Enviado: 15 de novembro de 2022 16:42 Para: ***@***.***> Cc: José Miguel Silva Ferreira ***@***.***>; ***@***.***> Assunto: Re: [compomics/peptide-shaker] Peptide-shaker doesn't progress from "Importing PSMs from mgf.comet.pep.xml.gz" (Issue #496) Não costuma receber e-mails de ***@***.*** Saiba por que motivo isto é importante<https://aka.ms/LearnAboutSenderIdentification> If PeptideShaker is stuck at that particular step for long, you can cancel the process and have a look at the PeptideShaker log file. You can find it from the PeptideShaker Welcome dialog > Settings & Help > Help > Bug Report. If you share that file here we can hopefully figure out what is going on. — Reply to this email directly, view it on GitHub<#496 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4GQI77JRGUAAD6SCGWDTSDWIO4OXANCNFSM6AAAAAASBD2I6U>. You are receiving this because you authored the thread.Message ID: ***@***.***> Tue Nov 15 15:07:23 GMT 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 6524764160. Total amount of memory in the Java virtual machine: 128974848. Free memory: 85150896. Java version: 1.8.0_341. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_341 os.name: Windows 10 memory: 68.2/163.1 processors available: 8 useCommandThread: false Tue Nov 15 15:16:37 GMT 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 6524764160. Total amount of memory in the Java virtual machine: 128974848. Free memory: 82539344. Java version: 1.8.0_341. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_341 os.name: Windows 10 memory: 66.3/163.1 processors available: 8 useCommandThread: false Tue Nov 15 15:17:36 GMT 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 6524764160. Total amount of memory in the Java virtual machine: 128974848. Free memory: 85192296. Java version: 1.8.0_341. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_341 os.name: Windows 10 memory: 66.2/163.1 processors available: 8 useCommandThread: false Tue Nov 15 15:18:28 GMT 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 6524764160. Total amount of memory in the Java virtual machine: 128974848. Free memory: 83195552. Java version: 1.8.0_341. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_341 os.name: Windows 10 memory: 66.3/163.1 processors available: 8 useCommandThread: false https://www.ebi.ac.uk/pride/ws/archive/project/count org.springframework.web.client.HttpClientErrorException$NotFound: 404 : "{<EOL> "timestamp" : 1668525575132,<EOL> "status" : 404,<EOL> "error" : "Not Found",<EOL> "message" : "No message available",<EOL> "path" : "/pride/ws/archive/v2/project/count"<EOL>}" at org.springframework.web.client.HttpClientErrorException.create(HttpClientErrorException.java:113) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:168) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:122) at org.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63) at org.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:819) at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:777) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:711) at org.springframework.web.client.RestTemplate.getForEntity(RestTemplate.java:361) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$33.run(PrideReshakeGUI.java:2523) Tue Nov 15 15:40:44 GMT 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 6524764160. Total amount of memory in the Java virtual machine: 128974848. Free memory: 113195176. Java version: 1.8.0_341. java.io.IOException: Server returned HTTP response code: 500 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Triticum aestivum&format=tab&columns=id at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1207) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:243) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1467) java.io.IOException: Server returned HTTP response code: 500 for URL: https://rest.uniprot.org/taxonomy/sort=score&desc=&compress=no&query=Triticum turgidum subsp. durum&format=tab&columns=id at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.downloadMapping(UniprotTaxonomy.java:123) at com.compomics.util.experiment.biology.taxonomy.mappings.UniprotTaxonomy.getId(UniprotTaxonomy.java:177) at com.compomics.util.parameters.identification.advanced.GeneParameters.setBackgroundSpeciesFromFastaSummary(GeneParameters.java:160) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1207) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:243) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1467) Tue Nov 15 16:47:27 GMT 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 6524764160. Total amount of memory in the Java virtual machine: 128974848. Free memory: 83616136. Java version: 1.8.0_341. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_341 os.name: Windows 10 memory: 66.3/163.1 processors available: 8 useCommandThread: false

[hbarsnes]

I don't see any errors in the log file related to the progress halting when importing the PSMs. Would it be possible for you to share the SearchGUI output file with me so that I can try to reproduce the issue on my end?

[MigRibe]

Of course. Many thanks. Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows De: Harald ***@***.***> Enviado: 15 de novembro de 2022 21:48 Para: ***@***.***> Cc: José Miguel Silva Ferreira ***@***.***>; ***@***.***> Assunto: Re: [compomics/peptide-shaker] Peptide-shaker doesn't progress from "Importing PSMs from mgf.comet.pep.xml.gz" (Issue #496) Não costuma receber e-mails de ***@***.*** Saiba por que motivo isto é importante<https://aka.ms/LearnAboutSenderIdentification> I don't see any errors in the log file related to the progress halting when importing the PSMs. Would it be possible for you to share the SearchGUI output file with me so that I can try to reproduce the issue on my end? — Reply to this email directly, view it on GitHub<#496 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4GQI73UYGE5JYUSY7I7TUTWIQAJBANCNFSM6AAAAAASBD2I6U>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[MigRibe]

searchgui_out.zip

[hbarsnes]

Thanks for sharing the SearchGUI zip file! However, in order to try loading the data I will also need the spectrum and FASTA files. Any chance you could share those as well?

[MigRibe]

Hi, Link with raw file and fasta. Thanks https://we.tl/t-9f50pFS7Lf Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows De: Harald ***@***.***> Enviado: 16 de novembro de 2022 20:20 Para: ***@***.***> Cc: José Miguel Silva Ferreira ***@***.***>; ***@***.***> Assunto: Re: [compomics/peptide-shaker] Peptide-shaker doesn't progress from "Importing PSMs from mgf.comet.pep.xml.gz" (Issue #496) Não costuma receber e-mails de ***@***.*** Saiba por que motivo isto é importante<https://aka.ms/LearnAboutSenderIdentification> Thanks for sharing the SearchGUI zip file! However, in order to try loading the data I will also need the spectrum and FASTA files. Any chance you could share those as well? — Reply to this email directly, view it on GitHub<#496 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4GQI74QZQRRB2XNAETSYRLWIU6ZLANCNFSM6AAAAAASBD2I6U>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[hbarsnes]

Thanks again! Any chance you can share the mgf file C:\Gui\MS\Glutenmgf.mgf instead of the raw file? (As I'm having some issues with the spectrum titles not matching yours if I do the conversion myself.)

[MigRibe]

https://we.tl/t-Jc3VXihQPr
Many thanks

[hbarsnes]

Your data initially loaded fine on my end without any issues. However, when I downgraded my Java version to the same as the one you are using, I was finally able to reproduce the issue. I would therefore recommend that you upgrade your Java version to a more recent version and see if that solves the problem. You can find the most recent versions here: https://adoptium.net/temurin/releases. After upgrading, you can check and set the Java version used in PeptideShaker via the Welcome dialog > Settings & Help > Settings > Java Settings.

By the way, it seems like your FASTA file does not contain any decoy sequences? Without this PeptideShaker will not be able to calculate the FDR for your dataset and you cannot be sure which identifications to trust. Decoys can easily be added in SearchGUI when selecting a FASTA file. Simply click yes to the question of whether you would like to add decoys. Note that you would then have to repeat the search before later loading the data in PeptideShaker.

[MigRibe]

Dear Harald, Thanks for your email. I will try with other java version as soon as possible, and I will give you my feedback. Yes, I am aware, but I am trying everything to get the program to work. Enviado do Correio<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows De: Harald ***@***.***> Enviado: 16 de novembro de 2022 22:45 Para: ***@***.***> Cc: José Miguel Silva Ferreira ***@***.***>; ***@***.***> Assunto: Re: [compomics/peptide-shaker] Peptide-shaker doesn't progress from "Importing PSMs from mgf.comet.pep.xml.gz" (Issue #496) Your data initially loaded fine on my end without any issues. However, when I downgraded my Java version to the same as the one you are using, I was finally able to reproduce the issue. I would therefore recommend that you upgrade your Java version to a more recent version and see if that solves the problem. You can find the most recent versions here: https://adoptium.net/temurin/releases. After upgrading, you can check and set the Java version used in PeptideShaker via the Welcome dialog > Settings & Help > Settings > Java Settings. By the way, it seems like your FASTA file does not contain any decoy sequences? Without this PeptideShaker will not be able to calculate the FDR for your dataset and you cannot be sure which identifications to trust. Decoys can easily be added in SearchGUI when selecting a FASTA file. Simply click yes to the question of whether you would like to add decoys. Note that you would then have to repeat the search before later loading the data in PeptideShaker. — Reply to this email directly, view it on GitHub<#496 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A4GQI73E3AAOQPT45LWDRJ3WIVPW5ANCNFSM6AAAAAASBD2I6U>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[MigRibe]

Dear Harald,
I followed your advice and I managed to get to the end of the peptideshaker analysis using the comet. Many thanks!
As for Amanda, it seems to have stucked; about 4 hours waiting without leaving 33% in peptideshaker (the file is the same). The bug log is attached.
PeptideShaker 2.2.17 log.txt

[hbarsnes]

Great to hear that you can now load the Comet data!

As for the MS Amanda issue, I don't see any explanations for this in the log file. Would you be able to share the SearchGUI zip file again?