brianjohnhaas
commented
10 months ago 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.
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.
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
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 calledGCA_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.