Description
Praveen Raj's profile photo
Praveen Raj
7:13 PM (5 minutes ago)
to MITObim-users
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