Panic runtime error in PhilosopherDbAnnotate

[gigi-mt]

Dear FragPipe team. I am re-running an analysis of two TMT11plex sets on FragPipe, same parameter as before, just with a custom made FASTA, decoys were added using FragPipe. MSFragger, Percolator and ProteinProphet are executed without warnings or errors. There is, however, a problem with Philosopher. I had received a warning for philosopher.exe about .meta\meta.bin not being found, and the dbannotate step is being aborted giving a panic: runtime error: index out of range [2] with length 0.

I am using the latest Philosopher version and emptied the FragPipe cache but I still receive the same error. Does it have to do with the FASTA file?

Here is the log report. log_2022-03-14_08-12-29.txt

Thanks for your help, G

[prvst]

ProteinProphet seems to work fine before the error, which shows the workspace is there. Try removing all empty spaces from your database name (and every folder), and try again.

[prvst]

Also, please send me your database file, I want to take a look at it

[prvst]

@gigi-mt I don't accept files sent to my personal email, please upload your file here (https://www.dropbox.com/request/T4wVIVH43OjS6du48TEK)

[gigi-mt]

I ran it again after removing empty spaces in the name of the FASTA file but get the same error. The database was uploaded to the provided dropbox link. Thanks. G log_2022-03-14_12-30-47.txt

[prvst]

Can you tell me how you came across to this database file? The Uniprot headers are changed in a way that the program cannot understand them.

[gigi-mt]

It is a canonical FASTA downloaded from UniProt and contains experimental sequences of mutated proteins written in the regular FASTA format. To distinguish between mutated and canonical proteins, the mutated UniProt accession contains the amino acid change. Decoy sequences were added using FragPipe, and make up 50% of the FASTA file.

The database works well with other proteomics tools.

From: Felipe da Veiga Leprevost @.> Sent: Monday, March 14, 2022 12:37 PM To: Nesvilab/FragPipe @.> Cc: gigi-mt @.>; Mention @.> Subject: Re: [Nesvilab/FragPipe] Panic runtime error in PhilosopherDbAnnotate (Issue #622)

Can you tell me how you came across to this database file? The Uniprot headers are changed in a way that the program cannot understand them.

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/622#issuecomment-1067040912, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ2EY3UMJ2ZCUYPPU5EK3TTU75TMBANCNFSM5QVMPLEQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.**@.>>

[prvst]

That's because the other proteomics you used are not parsing the information from the headers like we do. The problem is in the header of your added sequences:

Change this: sp|Q53EL9_R523H|R523H SEZ6_HUMAN missense_variant GN=SEZ6

To this: sp|Q53EL9_R523H|SEZ6_HUMAN missense_variant GN=SEZ6

Please fix all the entries you added that have the same pattern.

[gigi-mt]

Ok. I will try it and will get back to you. Thanks.

From: Felipe da Veiga Leprevost @.> Sent: Monday, March 14, 2022 12:47 PM To: Nesvilab/FragPipe @.> Cc: gigi-mt @.>; Mention @.> Subject: Re: [Nesvilab/FragPipe] Panic runtime error in PhilosopherDbAnnotate (Issue #622)

That's because the other proteomics you used are not parsing the information from the headers like we do. The problem is in the header of your added sequences:

Change this: sp|Q53EL9_R523H|R523H SEZ6_HUMAN missense_variant GN=SEZ6

To this: sp|Q53EL9_R523H|SEZ6_HUMAN missense_variant GN=SEZ6

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/622#issuecomment-1067050838, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ2EY3VETJH6ETFV37JATFLU75UOVANCNFSM5QVMPLEQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.**@.>>

[gigi-mt]

I made the changes to the FASTA as recommended and ran the workflow but get the same error.

I had also tried a FASTA downloaded in FragPipe, and get the same issue.

log_2022-03-14_16-15-53.txt

[prvst]

A FASTA file downloaded from UniProt should not give any issues, we use them routinely. Which organism did you fetch?

[gigi-mt]

Homo sapiens. See attached.

2022-03-14-decoys-reviewed-contam-UP000005640.zip

[prvst]

According to your most recent log, you used 2022-03-14-decoys-2022_0314_Canonical_WES_FASTA.fasta.fas

[gigi-mt]

Yes, that is correct. As I mentioned, after the corrected custom FASTA (2022-03-14-decoys-2022_0314_Canonical_WES_FASTA.fasta.fas) failed again , I ran the human UniProt FASTA fetched from FragPipe receiving the same error as with my custom FASTA.

I can share the the custom FASTA with you or any other file of this search if this helps figuring out the cause.

Thanks.

From: Felipe da Veiga Leprevost @.> Sent: March 15, 2022 4:15 PM To: Nesvilab/FragPipe @.> Cc: gigi-mt @.>; Mention @.> Subject: Re: [Nesvilab/FragPipe] Panic runtime error in PhilosopherDbAnnotate (Issue #622)

According to your most recent log, you used 2022-03-14-decoys-2022_0314_Canonical_WES_FASTA.fasta.fas

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/622#issuecomment-1068425929, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQ2EY3SG422XANRJCL32JZLVADVURANCNFSM5QVMPLEQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.**@.>>

[prvst]

@gigi-mt Please reset all parameters and check all fields, folders, and settings again. The Uniprot FASTA should always work, especially the human proteome one. If even though you still have errors, please send me the log and the human proteome you got from UniProt, and I'll double check for you.

[gigi-mt]

Reinstalling FragPipe and it's components for the third time did the trick. UniProt human DB and my custom DB ran without a problem. Thanks for your support fixing this.