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snijderlab / stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling
MIT License
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error in basic search #241

Closed pikiton closed 10 months ago

pikiton commented 10 months ago

Screenshot 2023-11-08 014042

pikiton commented 10 months ago

search in monoclonal work good with this file from X+. Files in attachment AAV_denovo_X_50.csv basicAAV.txt

douweschulte commented 10 months ago

Thanks for raising the issue! I am sorry for the crash, the issue is that the file you specified in the segment (../datasets/report-monoclonal.fasta) does not exist. After this error the code is left in a broken state and tries to detect other ways in which parsing can go wrong which leads it to this crash. If this does not fix your problem please let me know. I will take a look if this error is still in my development version and fix it there if applicable.

douweschulte commented 10 months ago

I just checked and the development version has this issue already patched. If you want you could move to this version, which also contains some other improvements. (Please note that the command line interface has changed, you now have to type stitch run <file> instead of stitch <file>).

The nightly version can be found on the github actions tab and then pick the latest one, scroll down and get the version for your architecture.