index builder requires massive memory and mapping fails about hisat2

[infphilo]

HISAT2-build used about 160 GB of RAM when building indexes using the human reference genome and 12.3 million common SNPs, so you may need a machine with 256 GB of RAM (or something like that) to build indexes for the hamster genome.

[cfblaeb]

So I actually did build the index on a much large machine.
However when I ran hisat2 with the above code for alignment, nothing seemed to happen. No output, constant use of 1 core and a few gigs of memory.

[misik]

I'm trying to build an index for C. elegans genome using the command below:

$HISAT2_HOME/hisat2-build Caenorhabditis_elegans.WBcel235.dna.toplevel.fa -ss splice_sites.txt and --exon exon.txt C_elegans

It builds an index in under 2 minutes but when I use hisat2 inspect --ss --exon C_elegans, I see that splice sites and exon info is not included in the index. Should I add other options to the script for this to work? Do you think the reason can be the difference between chromosome names between human and C. elegans?

Would it be possible for you to provide hisat2 indexes for C. elegans in your website? These are the ensembl files for latest fasta and gtf for C. elegans.

ftp://ftp.ensembl.org/pub/release-83/fasta/caenorhabditis_elegans/dna/
ftp://ftp.ensembl.org/pub/release-83/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.83.gtf.gz

head splice_sites.txt
I 4357 5194 -
I 5295 6036 -
I 6326 9726 -
I 9845 10094 -
I 10584 11617 +
I 11556 11617 +
I 11560 11617 +
I 11560 11622 +
I 11685 14949 +
I 11688 14950 +

head exons.txt
I 3746 3908 -
I 4118 4357 -
I 5194 5295 -
I 6036 6326 -
I 9726 9845 -
I 10094 10229 -
I 10412 10584 +
I 11494 11560 +
I 11617 11688 +
I 14949 15159 +

[kouroshz]

I ran into the same issue while building index for human hg38 using a gff annotation file downloaded from Ensemble. hisat built kept adjusting the memory (I had 64Gb) and finally finished. However, the subsequent use of hisat2 for alignment seems to be stuck with steady use of 1 core.

Remark: Some of the index file seem to be missing. I get 1,2,3,4,7,8 but not 5 and 6.