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

[Andreas Tille]

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