Comments (2)
Thanks for the detailed info!
First I need to reproduce the problem so that I can know where to put warning or error messages. How did you get those extra MHC (or HLA) sequences?
from hisat2.
We are using Ensembl's GRCh37, ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz.
Here I extracted all main chromosomes plus HSCHR6_MHC* sequences (7x).
I ran hisat2-build
with --ss
and --exon
. As it successfully created the index when I ran hisat2-build
on a "himem machine", I assume my colleague ran out of memory on a less potent server. Nevertheless he wasn't aware of any error occuring in the build process... so it was probably not very obvious ;-)
from hisat2.
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from hisat2.