Nathan Weeks

Hi @francicco , are your `--query` and `--target` sequences available for download so I can attempt to reproduce?

@sagnikbanerjee15 : could you provide example `--query` and `--target` sequences (can be uploaded to, e.g., Box if large), as well as the exonerate command used, so I can attempt to...

@sagnikbanerjee15: I was unable to reproduce the segfault using exonerate v2.4.0 (compiled from source, using a method similar to the one in the new [Dockerfile](https://github.com/nathanweeks/exonerate/blob/master/Dockerfile)), and executed with `-c 16`....

> are you aware of this forked repo? > > https://github.com/hotdogee/exonerate-gff3 which is an improved version of exonerate-2.2.0 with GFF3 format output support > > Maybe you could unite the...

@bwprice Could provide an example exonerate command & input files from the MGE workflow? That would help pinpoint the issue.

It appears MGE supports a debug mode: https://github.com/cmayer/MitoGeneExtractor/blob/552c04440de36d2036d10412dbaa5e7d84b59c04/MitoGeneExtractor.cpp#L1096-L1100 Could you try enabling this, and provide an example of an exonerate command string that "fails", and attach the query & target...

Would you be able to provide some input data that replicates the problem, as well as the exonerate version (e.g., git commit SHA-1) and arguments used?

@leicray Thanks for the report. Was this error observed when using exonerate built from the master branch? (see https://github.com/nathanweeks/exonerate/issues/5#issuecomment-1068141590)

@leicray Apologies for the slow follow-up---I reproduced the output you observed in my environment. I'll need to spend some additional time in a debugger to understand the code involved and...

> Have you had time to debug the numbering issue yet? I spent a debugging session last summer mostly reacquainting myself with the use of gdb to debug exonerate, but...