[Debian-med-packaging] Bug#1029202: snippy: Error when using snpeff 5.1

[Andreas Tille]

Package: snippy
Version: 4.6.0+dfsg-1
Severity: important
X-Debbugs-Cc: Pierre Gruet <pgt at debian.org>

Hi,

I was informed that snippy is not behaving nicely in all cases when
snpeff 5.1 is used.  A colleague is rather using it successfully with
snpeff 5.0.  You can verify this with the following test script:


#!/bin/sh
# create tmp dir
TMPDIR=$(mktemp -d /tmp/snippyXXXXX)
cd $TMPDIR
# download public read data
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR201/004/SRR2014554/SRR2014554_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR201/004/SRR2014554/SRR2014554_2.fastq.gz
# download reference data
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gbff.gz
gunzip GCF_000005845.2_ASM584v2_genomic.gbff.gz
mkdir tmp

set -x
snippy --cpus 4 --ram 20 --tmpdir ./tmp --reference GCF_000005845.2_ASM584v2_genomic.gbff --R1 SRR2014554_1.fastq.gz --R2 SRR2014554_2.fastq.gz --outdir results --report --mincov 20


This script ends with:

...
[15:25:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[15:25:13] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
 build -c reference/snpeff.config -dataDir . -gff3 ref
[15:25:16] Error running command, check results/snps.log


Checking the end of the log gives:

$ tail results/snps.log 
        transl_table : 11
        translation : MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPPYANGSIHIGHSVNKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKDFIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSIDVAFQAVDQDALKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVESVMQRIGVTDYTILGTVKGAELELLRFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDDYVIGQKYGLETANPVGPDGTYLPGTYPTLDGVNVFKANDIVVALLQEKGALLHVEKMQHSYPCCWRHKTPIIFRATPQWFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISRQRTWGVPMSLFVHKDTEELHPRTLELMEEVAKRVEVDGIQAWWDLDAKEILGDEADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYLEGSDQHRGWFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVASTDYTGEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCAKAAQEDILKAYEAYDFHEVVQRLMRFCSVEMGSFYLDIIKDRQYTAKADSVARRSCQTALYHIAEALVRWMAPILSFTADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDAFWDELLKVRGEVNKVIEQARADKKVGGSLEAAVTLYAEPELSAKLTALGDELRFVLLTSGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQDVGKVAEHAEICGRCVSNVAGDGEKRKFA
        type : CDS
. File '/tmp/snippyBRsOJ/results/reference/./ref/genes.gff' line 30     'NC_000913      snippy  CDS     22391   25207   .       +       0       ID=b0026;eC_number=6.1.1.5;Name=ileS;codon_start=1;db_xref=UniProtKB/Swiss-Prot:P00956,ASAP:ABE-0000094,ECOCYC:EG10492,GeneID:944761;gene=ileS;gene_synonym=ECK0027%3B ilvS;locus_tag=b0026;product=isoleucine--tRNA ligase;protein_id=NP_414567.1;transl_table=11;translation=MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPPYANGSIHIGHSVNKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKDFIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSIDVAFQAVDQDALKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVESVMQRIGVTDYTILGTVKGAELELLRFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDDYVIGQKYGLETANPVGPDGTYLPGTYPTLDGVNVFKANDIVVALLQEKGALLHVEKMQHSYPCCWRHKTPIIFRATPQWFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISRQRTWGVPMSLFVHKDTEELHPRTLELMEEVAKRVEVDGIQAWWDLDAKEILGDEADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYLEGSDQHRGWFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVASTDYTGEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCAKAAQEDILKAYEAYDFHEVVQRLMRFCSVEMGSFYLDIIKDRQYTAKADSVARRSCQTALYHIAEALVRWMAPILSFTADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDAFWDELLKVRGEVNKVIEQARADKKVGGSLEAAVTLYAEPELSAKLTALGDELRFVLLTSGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQDVGKVAEHAEICGRCVSNVAGDGEKRKFA'
WARNING_TRANSCRIPT_NOT_FOUND: Too many 'WARNING_TRANSCRIPT_NOT_FOUND' warnings, no further warnings will be shown.
WARNING_TRANSCRIPT_ID_DUPLICATE: Transcript 'b4616' already added. File '/tmp/snippyBRsOJ/results/reference/./ref/genes.gff' line 3839  'NC_000913      snippy  ncRNA   3853118 3853190 .-       .       ID=b4616;Name=istR;db_xref=ECOCYC:G0-10201,GeneID:5061525;gene=istR;gene_synonym=ECK4425%3B istR-1%3B istR-2%3B psrA19;locus_tag=b4616;ncRNA_class=other;product=small regulatory RNA IstR-1'
WARNING_FRAMES_ZERO: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.
ERROR: CDS check file '/tmp/snippyBRsOJ/results/reference/./ref/cds.fa' not found.
ERROR: Protein check file '/tmp/snippyBRsOJ/results/reference/./ref/protein.fa' not found.
ERROR: Database check failed.



In contrast to this my colleage reported the script was working when
using snippy via conda environment:

# create the environment
mamba create -n snippy
# install snippy (version fixing of snpeff is essential to avoid a bug when using genbank files as reference
input)
mamba activate snippy
mamba install -y -c conda-forge -c bioconda -c defaults snpeff=5.0 snippy
# check installation
snippy --check
# deactivate environment
mamba deactivate


So we somehow need to find out the difference between snpeff 5.0 and 5.1
to make snippy working nicely with the Debian packaged snpeff.  May be
this could be discussed with upstream but I simply wanted to drop a
record here.

Kind regards
   Andreas.
-- System Information:
Debian Release: bookworm/sid
  APT prefers testing
  APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), (5, 'experimental'), (1, 'buildd-experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 6.0.0-2-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE:de
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages snippy depends on:
ii  any2fasta         0.4.2-2
ii  bcftools          1.16-1
ii  bedtools          2.30.0+dfsg-2
ii  bwa               0.7.17-7
ii  freebayes         1.3.6-2
ii  libbio-perl-perl  1.7.8-1
ii  libvcflib-tools   1.0.3+dfsg-2
ii  minimap2          2.24+dfsg-3
ii  parallel          20221122+ds-2
ii  perl              5.36.0-7
ii  samclip           0.4.0-4
ii  samtools          1.16.1-1
ii  seqtk             1.3-4
ii  snp-sites         2.5.1-2+b1
ii  snpeff            5.1+d+dfsg-2
ii  vt                0.57721+ds-3

snippy recommends no packages.

snippy suggests no packages.

-- no debconf information