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 "^+$")
reference.fa: A cleaned FASTA with a single-line header
Manifest file (simplified):
project = D_arctica_E823
job=genome,mapping,accurate
parameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no
readgroup
is_reference
data = reference.fa
strain = D_arctica_ref
readgroup = reads
data = reads.fastq
technology = solexa
strain = D_arctica_reads
Despite trying multiple FASTA formats and ensuring the FASTQ is properly interleaved, I receive the following error:
Tmp directory is not on a NFS mount, good.
Segmentation fault (core dumped)
Failure, wrapped MIRA process aborted.
I initially thought the issue stemmed from my input data, but after testing with the official MITObim GitHub test data, I encountered the exact same error.
I’d appreciate any advice or insights from others who may have encountered this issue or know potential workarounds.
Thank you in advance!
Best regards,
Praveen
Praveen Raj's profile photo
Praveen Raj
7:13 PM (5 minutes ago)
to MITObim-users
Hi,
I’m currently trying to run a mitochondrial assembly using MITObim within a Docker container (based on MIRA 4), and I consistently encounter a segmentation fault (core dumped) error during the MIRA mapping step.
Here are some details about my setup and what I’ve tried:
Platform: Ubuntu via WSL2 on Windows
Docker: Running MITObim in a custom Docker container with MIRA 4 installed
Input files:
reads.fastq: Interleaved Illumina paired-end reads (validated with grep "^@" and grep "^+$")
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