Groza Cristian

It seems that crash is in minimap2, due to the CIGAR exceeding a certain length. We will try passing the -L flag to minimap2 and push a new commit, to...

I pushed the commit in main. Please let us know if it worked.

Otherwise, it seems minimap2 has difficulty aligning your genomes. The CIGAR operation says that minimap2 is trying to hard clip more than 200 Mbp of sequence. Could you tell us...

I just finished reading the post you linked. Indeed, the problem could be samtools sort. You could try splitting the largest contigs in half to avoid the basepair limit.

Yes we should add it. We ourselves never encountered this issue, since it seems to be a result of an obscure limitation in htslib which samtools uses. On Thu, Sep...

Hi, This problem was actually caused by genome assemblies that were scaffolded and the gaps masked with long runs of N. You may fix this by breaking the gaps into...

Hi It's a bit difficult for me to track the bug without more information. It seems some step in annotating the VCF with repeats fails. Could you share `svim-asm_variants.vcf` from...

Hi May I see your `nextflow.config`?

Also, I pushed a commit that may fix the error in the tsd_report step. Can you please pull the latest version and try again?

I see you were on an older version of the config. Also try this nextflow.config: ``` manifest.defaultBranch = 'main' singularity.enabled = true singularity.autoMounts = true singularity.runOptions = '--contain --bind $(pwd):/tmp'...