Segmentation fault when running MIRA via MITObim Docker container

[Praveen Raj]

Hi,

 

I’m currently trying to run a mitochondrial assembly using MITObim within a Docker container (based on MIRA 4), and I consistently encounter a segmentation fault (core dumped) error during the MIRA mapping step.  

Here are some details about my setup and what I’ve tried:

• Platform: Ubuntu via WSL2 on Windows

• Docker: Running MITObim in a custom Docker container with MIRA 4 installed

• Input files:

  • reads.fastq: Interleaved Illumina paired-end reads (validated with grep "^@" and grep "^+$")

  • reference.fa: A cleaned FASTA with a single-line header

  Manifest file (simplified):

project = D_arctica_E823

job=genome,mapping,accurate

parameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no

readgroup
is_reference
data = reference.fa
strain = D_arctica_ref

readgroup = reads
data = reads.fastq
technology = solexa

strain = D_arctica_reads  

Despite trying multiple FASTA formats and ensuring the FASTQ is properly interleaved, I receive the following error:

Tmp directory is not on a NFS mount, good.

 Segmentation fault (core dumped) 

Failure, wrapped MIRA process aborted.

  I initially thought the issue stemmed from my input data, but after testing with the official MITObim GitHub test data, I encountered the exact same error.  

I’d appreciate any advice or insights from others who may have encountered this issue or know potential workarounds.

Thank you in advance!

Best regards,

Praveen