[Debian-med-packaging] Bug#1031465: snippy: FTBFS: make[2]: *** [Makefile:32: S1/snps.tab] Error 2

[Nilesh Patra]

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 <andreas at 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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