Segmentation fault with --Ivcf argument

This seems similar to https://github.com/fritzsedlazeck/Sniffles/issues/31

sniffles runs, happily printing out progress, and at the end I get:

                [...........]
		# Processed reads: 6170000
		# Processed reads: 6180000
		# Processed reads: 6190000
	Switch Chr chrY
		# Processed reads: 6200000
Print:
Finalizing  ..
/bin/bash: line 1: 35826 Segmentation fault      (core dumped) sniffles --mapped_reads ngmlr_alignment/anon.bam --vcf sniffles_genotypes/anon.vcf --threads 12 --Ivcf sniffles_combined/calls.vcf 2> logs/sniffles_genotype/anon.log

No vcf is produced, but I can see a “anon.vcf_tmp_genotype” binary file in the output directory.

Unfortunately, I cannot share my input data. The alignment is done using ngmlr, the vcf for --Ivcf is made using Survivor after using sniffles without --Ivcf (which did not lead to this problem).

What can I do to try to debug this?

[wdecoster]

Oh well, that took even longer than expected, but now I can confirm that there is no longer a segmentation fault in this version. Perhaps it’s worth creating another release to allow updating the bioconda version?

[wdecoster]

Absolutely great service.

While I’m rerunning “the workflow” I also changed the reference genome for ngmlr so it will take a while before I can report how things go with the latest version - so no need to stay awake ^_^