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UCL / cathpy

Python Bioinformatics Toolkit for CATH (Protein Classification Database @ UCL)
http://cathdb.info
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Unable to parse/process resolve-hits input data file "Pfam-A_notc_18.out" of format hmmsearch_out. Error was: Failed to parse a number (of type j) from CS #13

Closed bordin89 closed 3 years ago

bordin89 commented 3 years ago

Hello CATH! This error is thrown when I used cath-resolve-hits on the full output of hmmsearch against Pfam-A.

This is the command I ran

cath-resolve-hits.macos --min-dc-hmm-coverage=80 --worst-permissible-bitscore 25 --output-hmmer-aln --input-format hmmsearch_out fulloutput/Pfam-A_notc_18.out > crh/Pfam-A_notc_1e18.crh

The hmmsearch output is complete and the run was successful.

cath-resolve-hits output a regular crh file if I use the domtblout instead. Could it be that one of the flags that are specific to the hmmsearch_output are not compatible with Pfam or Pfam-style names?

sillitoe commented 3 years ago

Thanks - could you attach the (preferably smallest) version of input file that allows me to repeat the error?

sillitoe commented 3 years ago

Also, which version of hmmsearch?

bordin89 commented 3 years ago

Hi Ian, here's the link to the full output /cath/people2/ucbtnb4/tmp/Pfam-A_notc_18.out hmmsearch version 3.3

sillitoe commented 3 years ago

Thanks - looks like this has been fixed in the latest version of cath-resolve-hits - will upgrade the binaries included in this package

sillitoe commented 3 years ago

Fixed in #16 and released to pypi as v0.4.0

sillitoe commented 3 years ago

Could you check and close the issue if you're happy it has been fixed.

bordin89 commented 3 years ago

Just tested the new version, it works perfectly. Thanks a lot!