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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

Aborted execution on dotnet TransferUniProtModifications #199

Closed Stanley80 closed 3 years ago

Stanley80 commented 3 years ago

Dear Spritz Developers, thank you very much for your amazing work.

Today, we successfully installed Spritz in a custom conda environment of a CENTOS server. When we launched snakemake everything worked fine, but at the step 13 somethings happened.

We report the bottom part of log located in /mnt/datasets/spritz/variants/Homo_sapiens.GRCh38.100.spritz.log.

00:01:12 Predicting variants 00:01:12 Creating xml file /mnt/datasets/spritz/variants/Homo_sapiens.GRCh38.100.protein.xml with 365688 transcripts 00:03:21 done. 00:03:21 Logging 00:03:22 Checking for updates... 00:03:23 Done. Welcome to TransferModifications! Analyzing UniProt database data/uniprot/Homo_sapiens.protein.xml.gz and Unhandled exception. System.NullReferenceException: Object reference not set to an instance of an object. at TransferUniProtModifications.ProteinAnnotation.ParseCodingEffectsToXml(String codingEffectFilePaths, Int32 minPeptideLength, String organism) in /mnt/projects/Spritz/Spritz/TransferUniProtModifications/TransferUniProtModifications/ProteinAnnotation.cs:line 33 at TransferUniProtModifications.TransferUniProtModifications.Main(String[] args) in /mnt/projects/Spritz/Spritz/TransferUniProtModifications/TransferUniProtModifications/TransferUniProtModifications.cs:line 45 /usr/bin/bash: line 1: 73285 Aborted dotnet TransferUniProtModifications/TransferUniProtModifications/bin/Release/netcoreapp3.1/TransferUniProtModifications.dll -x data/uniprot/Homo_sapiens.protein.xml.gz -y /mnt/datasets/spritz/variants/Homo_sapiens.GRCh38.100.protein.xml

It seems to be a bug!!!

Can someone have the solution to this issue?

Thank you very much

acesnik commented 3 years ago

Thank you for reporting the bug. Yes, we've had a little trouble with the commandline version as of late (https://github.com/smith-chem-wisc/Spritz/issues/195), and fixing this functionality is the top priority for this project right now. I'll keep you posted!

acesnik commented 3 years ago

Hi again!

I believe this is actually due to the same issue we saw here: https://github.com/smith-chem-wisc/Spritz/issues/201. I believe we have resolved this one by updating mzLib, an underlying library for Spritz. Feel free to give this another shot.

Best regards,

Anthony

acesnik commented 3 years ago

I just double-checked that this works on my machine's commandline (macOS 11.1), and it does make it through this step.

Stanley80 commented 3 years ago

Thank you very much acesnik!!! I'll try it now

acesnik commented 3 years ago

Closing this for now. Feel free to reopen if the problem persists.

stsour commented 3 years ago

Hello @acesnik !

I would like to reopen this issue. I have just cloned the current Spritz release into my CENTOS server home drive. This is an access-protected server and I went through all the steps for offline computing. Everything worked until step 11.

I am running into the exact same issue as Stanley80, but I presume that the mzLib update is included in the latest release? For some reason, this is not solving the problem for me.

Would appreciate some assistance! Thanks.

acesnik commented 3 years ago

I was able to replicate this error earlier last week, and I believe it is fixed in https://github.com/smith-chem-wisc/Spritz/pull/211.

acesnik commented 3 years ago

Please reopen if you're still encountering it!