Error with guidescan enumerate

[Lukas-1]

Hi,

I'm excited to try out the new version of GuideScan, but I've been getting the following error:

guidescan enumerate ncbi-genomes-2022-12-21/hg38 -f Input_for_GuideScan2/input.csv -o Output_from_GuideScan2/output.csv
[guidescan2] [info] Loading genome index at "ncbi-genomes-2022-12-21/hg38".
[guidescan2] [info] Successfully loaded genome index.
[guidescan2] [info] Loading kmers.
[guidescan2] [info] Read in 40664 kmer(s).
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr: __pos (which is 1) > this->size() (which is 0)
Aborted (core dumped)

I downloaded the RefSeq .fna file for hg38 from this page https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/, and indexing seemed to complete successfully. Do you know what might be causing the issue?

Thanks,
Lukas

[vineetbansal]

I think it might be that you don't have anything in the PAM column in your input.csv? We noticed this issue recently and are about to patch it up.

[Lukas-1]

That fixed it! Thanks a lot for the quick reply, and for creating and maintaining this great tool!

[vineetbansal]

Great - let me close this issue, but we'll fix the underlying issue in the next couple of days in guidescan which should make it work even in the absence of any PAMs.