Genome GRCh38 not detected

[micknudsen]

Hi,

I'm trying to generate a library from scratch based on GRCh38 with some regions masked (GRC exclusions). Very early in the main script, the reference genome FASTA is copied to a file with the more generic name ref_genome.fa, and then the genome build is not detected in the masking step.

https://github.com/NCIP/ctat-genome-lib-builder/blob/1cf500c07a67c0240228b8f9c245c0db3e507e4f/util/mask_confounding_features_from_genome.pl#L59

As a consequence, the script dies with the error message Error, didn't locate PAR features in $gencode_gtf. My original input FASTA file is called GCA_000001405.15_GRCh38_no_alt_analysis_set.GRC_exclusions_masked.fasta.

I have made a hack and changed the line to my $IS_GRCH38 = 1, and now everything seems to be running smoothly.

[brianjohnhaas]

Terrific! Leave this open and I'll work on improving the interface to this at some point.

…

On Tue, Jan 9, 2024 at 1:41 AM Michael Knudsen ***@***.***> wrote: Hi, I'm trying to generate a library from scratch based on GRCh38 with some regions masked (GRC exclusions). Very early in the main script, the reference genome FASTA is copied to a file with the more generic name ref_genome.fa, and then the genome build is not detected in the masking step. https://github.com/NCIP/ctat-genome-lib-builder/blob/1cf500c07a67c0240228b8f9c245c0db3e507e4f/util/mask_confounding_features_from_genome.pl#L59 As a consequence, the script dies with the error message Error, didn't locate PAR features in $gencode_gtf. My original input FASTA file is called GCA_000001405.15_GRCh38_no_alt_analysis_set.GRC_exclusions_masked.fasta. I have made a hack and changed the line to my $IS_GRCH38 = 1, and now everything seems to be running smoothly. — Reply to this email directly, view it on GitHub <#18>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3PCVKYOSWQV67FWRLYNTRBHAVCNFSM6AAAAABBSSWJSSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCNZSGU4DMMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[matej-zatko]

I was struggling with the same issue, thank you @micknudsen for providing the workaround. Would love to see this bug fixed as it prevents the library from being built.