Problem hisat2-build

[hadlichFBN]

Good morning hisat2-experts,

I really want to use hisat2, but I run into trouble building up an index on a compute server with enough cpus, disk space and ram using this command:

~/hisat2-2.0.3-beta/hisat2-build -p 60 --ss Sscrofa10.2.84.splicesites.txt --exon Sscrofa10.2.84.exons.txt --large-index --haplotype Sus_scrofa.10.2.84.haplotype --snp Sus_scrofa.10.2.84.snp -f Sscrofa10.2.84.fa Sscrofa10.2.84

Without snp and haplotype information this job succeeds! Snp and haplotype files were generated successfully with hisat2_extract_snps_haplotypes_VCF.py. Data origin is ensembl.
These are the last lines of the console output:

FINISHED RECURSIVE SORTS: 420
SORT, Make index: 522
TOTAL: 2698
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 1042314871
fchr[G]: 1795533585
fchr[T]: 2547556460
fchr[$]: 3591534603
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 2227544711 bytes to primary GFM file: Sscrofa10.2.84.1.ht2l
Wrote 1783815948 bytes to secondary GFM file: Sscrofa10.2.84.2.ht2l
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted

(Temporary) output files are: Sscrofa10.2.84.{1..8}.ht2l

I am very pleased about every helping advice.

Cheers, Frieder

[infphilo]

This problem might have been fixed in the latest version of HISAT2 2.0.4. Please feel free to let us know if you still encounter this issue. I'll close the issue for now.