Question on mouse index, bowtie2-build not indexing properly?

[josruirod]

Hi, so I've used bowtie2 many times before, but I have now encountered an unexpected problem with the indexing process on the last version (v2.4.5). So I downloaded the GRCm39 primary assembly from ensembl, and tried to index with:

bowtie2-build --threads 20 Mus_musculus.GRCm39.dna.primary_assembly.fa Mus_musculus.GRCm39.dna.primary_assembly.fa_bowtie2_index &> Mus_musculus.GRCm39.dna.primary_assembly.fa_bt2_index.log

No apparent errors in the log (I attach it) and the .1 to .4 files, rev.1 and rev.2 were created. When I try to align, no apparent errors but ~0% alignment rate. However, when I downloaded the pre-built index for GRCm39from the bowtie2 page, and aligned with the same instruction, got ~95% alignment.

Could you provide any assistance on what's the issue with the indexing step? Will need to do that soon with other species without not pre-built indexes available.

Thanks for the kind support

Mus_musculus.GRCm39.dna.primary_assembly.fa_bt2_index.log