bowtie2-index stuck in Entering Ebwt loop

BenLangmead / bowtie2

A fast and sensitive gapped read aligner

GNU General Public License v3.0

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bowtie2-index stuck in Entering Ebwt loop #493

Closed imk1 closed 1 month ago

imk1 commented 1 month ago

I have been trying to run bowtie2-index and found that it keeps getting stuck in "Entering Ebwt loop." I am using bowtie2 version 2.3.4.3. It sometimes gets stuck there for hours, even when I alot >30GB of RAM. I have found that it can get stuck on fasta files as small as a few hundred lines. Might someone be able to help me out with this? Thanks!

imk1 commented 1 month ago

I think that we might have solved the problem. To do this, we upgraded bowtie2 from version 2.3.4.3 to 2.5.4. In order to get this upgrade to work, we first had to upgrade libgcc-ng to version 12.