Package: snippy Version: 4.6.0+dfsg-1 Severity: important X-Debbugs-Cc: Pierre Gruet <p...@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
