(ERR): bowtie2-align died with signal 11 (SEGV) (core dumped)

[a-kroh]

Hi,

I am using Bowtie2 often, it is a great program. Today, when starting a read mapping run, however, I came across a cryptic error message that took me some time to figure out. Immediately after calling the program I got the following message:

(ERR): bowtie2-align died with signal 11 (SEGV) (core dumped)

A Google search did not help much, except turning up forum entries where people had similar issues, but no solution.

After a while I found that the reason was my own fault - a tiny typo in the name of readpool files. It would be great if in future versions a specific error message could be displayed in such cases, as is the case when there is a typo in the name of the Bowtie2 index (or the index is missing).

All the best Andreas

[ch4rr0]

Did you try rerunning your alignment with the *-debug binary? The assert statements that would typically catch such errors are disabled in the optimized (non-debug) binaries. If the debug binary fails to catch this issue, please share some sample input, so that we can recreate the issue and include the necessary assertions.

[dhrpa]

Hi, I have a similar issue. I tried running bowtie2 to remove human contamination from my reads and got the following error: bowtie2-align died with signal 11 (SEGV). Can you help me with this?

I had originally trimmed my reads using trimmomatic and was using the paired reads as input for Bowti2.

Thank you

[jianshu93]

(ERR): bowtie2-align died with signal 11 (SEGV) Still this bug in 2.4.3

Jianshu

[northNomad]

I also encountered this bug using v2.4.5.

It only happens when I use a long index (.bt21). Using the same FASTQs with a short index works just fine.

[jianshu93]

Hello Team,

I did not expect this but from v 2.3 to v2.4.5.1 this happens all the time:

Jianshus-MBP-2:test_data jianshuzhao$ bowtie2 -x ./all_mag.fasta -f --interleaved ./T4AerOil_sbsmpl5.fa.gz -S all_mag_bowtie2.sam --threads 4 (ERR): bowtie2-align died with signal 11 (SEGV)

Both apple M1 pro and intel processor were tested and this happens. Without the --thread 4 it is ok, meaning 1 thread is ok but multithreads is problematic.

Please carefully check the tbb multithreaded implementation (or pthreads). bowtie2 was installed via homebrew.

Thanks,

Jianshu

[lateral-search]

Hi, I got this error a few times in the past, and initially it looks like segmentation fault, I checked my hardware resources and in my opinion happened when the system runs out of memory resources, ram or disk, wherever doesn't matters. So not a bad idea to have hw resources meter apps monitoring while bioinformatics analysis are running ;) Conclusion: probably not a bug, just a regular system exception.

Andy