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we created a GRCh37 index (with some extra MHC haplotype sequences included). There was no "eye-catching" error and we went on aligning or datasets with hisat2 against this index.
These jobs were running on one single cpu core (-p 12 was used) "forever". strace was just dumping read(6, "", 4096) = 0 ... and obviously nothing happened ...
So we took a closer look at the index. There were two files missing (5+6).
In case of an error you could make the error message more "eye-catching" during or after building the index. You could even remove the incomplete index to make people aware that there was sth. serious going wrong.
the alignment process (or the wrapper hisat2) should probably check if the index is complete and not corrupted.
Great tool though, .. just my 2p ;-)
Sven
The text was updated successfully, but these errors were encountered:
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 ;-)
Hi,
we created a GRCh37 index (with some extra MHC haplotype sequences included). There was no "eye-catching" error and we went on aligning or datasets with
hisat2
against this index.These jobs were running on one single cpu core (-p 12 was used) "forever".
strace
was just dumpingread(6, "", 4096) = 0
... and obviously nothing happened ...So we took a closer look at the index. There were two files missing (5+6).
Great tool though, .. just my 2p ;-)
Sven
The text was updated successfully, but these errors were encountered: