Hi Pjotr, in contrast to the bug reporter I get in my unstable chroot
... [15:53:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.16 [15:53:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6 [15:53:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.1 ... which looks good regarding the version check of freebayes. However later on the test ends up in: Loaded 3 sequences totalling 317336 bp. Loading mask bed file: example.bed Will mask 8 regions totalling 3101 bp ~ 0.98% 0 S1 snp=0 del=0 ins=0 het=0 unaligned=9643 1 S2 snp=0 del=0 ins=0 het=81 unaligned=9428 2 S3 snp=0 del=0 ins=0 het=0 unaligned=9376 3 S4 snp=0 del=0 ins=0 het=0 unaligned=9707 Opening: core-mask.tab Opening: core-mask.vcf Processing contig: LBB_contig000001 Processing contig: LBB_contig000002 Processing contig: LBB_contig000003 Masking alignment at 8 regions Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln Warning: No SNPs were detected so there is nothing to output. ERROR: Could not run: snp-sites -c -o core-mask.aln core-mask.full.aln I'm not sure whether this might be related to some previous freebayes call (which is the only package in the list of dependencies that has changed) or whether there is some other problem. I think it is worth investigating since snippy might be an interesting test suite for a whole bunch of packages. Kind regards Andreas. -- http://fam-tille.de
