Segmentation fault: 11 on modbam files (ONT)

Machadum commented 2 months ago

Hi again

I am a newbie. I have modbam files from ONT that I try to call SVs on but I have Segmentation fault: 11 error. Do you have an idea of what it could be? Also it does not indicate the avg DEL/INS ratios to start with, which worries me a bit.

sniffles --mapped_reads /Volumes/Rita/Pilot/output/SL7-1_bam_pass_merged_sorted.bam --vcf SL7-1.vcf --tmp_file /Volumes/Janet/sniffles/ --threads 8 --cluster  --genotype
Estimating parameter...
    Max dist between aln events: 53
    Max diff in window: 50
    Min score ratio: 2
    Avg DEL ratio: nan
    Avg INS ratio: nan
Start parsing...

[…]

    Writing SV calls
Segmentation fault: 11

Many thanks for your help

lfpaulin commented 2 months ago

Hello, @Machadum which version of sniffles are you using? It seems that you are using sniffles1 We recommend you to switch to sniffles2

Machadum commented 2 months ago

Hi thank you for your quick answer. The switch to sniffles2 unfortunately does not work:

conda update sniffles=2.3

Retrieving notices: ...working... done

CondaError: Invalid spec for 'conda update': sniffles=2.3
Use 'conda install' instead.

conda install sniffles=2.3

Channels:
 - bioconda
 - conda-forge
 - defaults
 - r
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - sniffles=2.3*

Current channels:

  - https://conda.anaconda.org/bioconda
  - https://conda.anaconda.org/conda-forge
  - defaults
  - https://conda.anaconda.org/r
  - https://repo.anaconda.com/pkgs/free

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

fritzsedlazeck / Sniffles

Segmentation fault: 11 on modbam files (ONT) #491