Apply fails with single input file

PNNL-CompBio / Snekmer

Pipeline to apply encoded Kmer analysis to protein sequences

BSD 3-Clause "New" or "Revised" License

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Apply fails with single input file #123

Open tnitka opened 6 months ago

tnitka commented 6 months ago

When running Apply with a single input file, Snekmer fails with the error message InvalidIndexError in line 292 of /qfs/people/nitk592/snekmer-main/Snekmer/src/snekmer/snekmer/rules/apply.smk: Reindexing only valid with uniquely valued Index objects

It's currently possible to work around this issue by splitting the input into 2 or more fasta files.

tnitka commented 6 months ago

This error also sometimes occurs even if the input sequences are split into multiple files. This might be Snekmer reading the same name for two sequences, which shouldn't be happening here as each sequence is uniquely labeled by profmark.

jjacobson95 commented 5 months ago

@tnitka would you be able to provide the same files you used? Haven't been able to reproduce this yet.