Closed Stanley80 closed 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!
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
I just double-checked that this works on my machine's commandline (macOS 11.1), and it does make it through this step.
Thank you very much acesnik!!! I'll try it now
Closing this for now. Feel free to reopen if the problem persists.
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.
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.
Please reopen if you're still encountering it!
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