Attempting to fix Pjotr's address. Pjotr: if you are reading this, could you comment on it?
Thanks Nilesh On Mon, 20 Feb 2023 17:21:59 +0100 Andreas Tille <andr...@an3as.eu> wrote: > 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 > >
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