I faced with strange error using GSNAP version 2023-03-24.

First, I normally created index for genome from fasta file containing 3 relatively short sequences (fragments of genes)

gmap_build -D ref_genomic_sequences/gmap_index -d index_name ref_genomic_sequences/genome.fasta

Then I tried to map reads on this reference using following command

gsnap -D ref_genomic_sequences/gmap_index -d index_name -n 1 -Q F_reads.fastq R_reads.fastq > gmap_res.sam

But gsnap crushed with the error

Allocating memory for localdb...insufficient memory

This is strange because 1) I works on a server with plenty of RAM and disk space 2) Reference sequence is short 3) Reads for mapping in fastq-files are not so much (~ 3M). Also I tried to map only 100 reads and recived the same error.

I tried different batch types (-B argument), tried to build suffix array during indexing (--sarray=1 argument for gmap_build).

The same reads and reference behave normally both in bwa and bowtie2, but not in gsnap. Anybody met with the same problem and know how to solve it?