Hi there,
I'm working with lofreq to call variants in a simulated bacterial dataset, and in some cases, lofreq call runs into a buffer overflow.
That's the command I used for calling:
lofreq call -f "path/to/reference/fasta" --call-indels -o "path/to/output.vcf" "path/to/bam/file.bam" 2> "path/to/log/file.log"
And that's the error message I've got:
*** buffer overflow detected ***: terminated
I've already inspected the BAM files, but they look normal. I'm using lofreq version 2.1.5, installed via conda, on Ubuntu 24.04.2 LTS. Has anyone had similar issues or/and maybe a workaround?
Thank you for your time and assistance!
Hi there,
I'm working with lofreq to call variants in a simulated bacterial dataset, and in some cases, lofreq call runs into a buffer overflow.
That's the command I used for calling:
lofreq call -f "path/to/reference/fasta" --call-indels -o "path/to/output.vcf" "path/to/bam/file.bam" 2> "path/to/log/file.log"And that's the error message I've got:
*** buffer overflow detected ***: terminatedI've already inspected the BAM files, but they look normal. I'm using lofreq version 2.1.5, installed via conda, on Ubuntu 24.04.2 LTS. Has anyone had similar issues or/and maybe a workaround?
Thank you for your time and assistance!