Bug#1029202: snippy: Error when using snpeff 5.1
Hi, since version 5.2.b is not worse than 5.1 (= upstream upgrade with the very same problematic output as version 5.1) I decided to update to the latest upstream version and pinged upstream again[1]. Kind regards Andreas. [1] https://github.com/pcingola/SnpEff/issues/455 -- http://fam-tille.de
Bug#1029202: snippy: Error when using snpeff 5.1
Hi Pierre, writing from some weak connection while traveling. Am Fri, Aug 25, 2023 at 02:30:45PM +0200 schrieb Pierre Gruet: > I found some time :-D > Upstream changed the location of the build-time tests, putting them in a > more canonical place. I updated the patches and d/rules accordingly. This is > all pushed to the Salsa repo. Thanks a lot. > However, the script you provided in the bug report [0] is still not working > with this newly packaged version 5.1+f+dfsg (tested locally), so probably we > should do as you suggested there [1] and provide 5.1+d+dfsg-really5.0+f in > unstable, as the script is working with version 5.0+f. > > Admittedly this is a step back for the library, but as least one would have > the use case of your colleagues working. If you still think this is a good > idea, I offer to finalize this step back. Network here is to weak to check for upstream tracker. I would add the action we take to the tracker and if we do not get any response we do so and roll back to 5.0+f. Thanks a lot for caring Andreas. PS: You probably will keep the current version in some branch on Salsa ... > [0] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1029202#5 > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1029202#37 -- http://fam-tille.de
Bug#1029202: snippy: Error when using snpeff 5.1
Hi Andreas, Le 24/08/2023 à 11:21, Andreas Tille a écrit : Hi Pierre, I just noticed that snpeff upstream has tagged a new release. I've injected the new tarball into Salsa Git but did not yet worked on the quilt patches that need to be adapted. If you throw an ENOTIME error I could see how far I might come with the changes. If you find some spare time for this issue I'd leave further changes to you. I found some time :-D Upstream changed the location of the build-time tests, putting them in a more canonical place. I updated the patches and d/rules accordingly. This is all pushed to the Salsa repo. However, the script you provided in the bug report [0] is still not working with this newly packaged version 5.1+f+dfsg (tested locally), so probably we should do as you suggested there [1] and provide 5.1+d+dfsg-really5.0+f in unstable, as the script is working with version 5.0+f. Admittedly this is a step back for the library, but as least one would have the use case of your colleagues working. If you still think this is a good idea, I offer to finalize this step back. Kind regards Andreas. Best, -- Pierre [0] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1029202#5 [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1029202#37 OpenPGP_signature.asc Description: OpenPGP digital signature
Bug#1029202: snippy: Error when using snpeff 5.1
Hi Pierre, I just noticed that snpeff upstream has tagged a new release. I've injected the new tarball into Salsa Git but did not yet worked on the quilt patches that need to be adapted. If you throw an ENOTIME error I could see how far I might come with the changes. If you find some spare time for this issue I'd leave further changes to you. Kind regards Andreas. -- http://fam-tille.de
Bug#1029202: snippy: Error when using snpeff 5.1
Hi, since upstream is not very quick in answering to questions in issues I had a look myself into the upstream repository and checked when the version string was bumped to the last release of the 5.0 series which is 5.0f. I found the commit[1] where REVISION was bumped to 'f'. The git log messages are usually pretty worthless "Project updated" is the most frequently used commit comment in the whole log. I simply checked out that commit[1], created a tarball from it and injected it into a new packaging branch 5.0f[2]. If we might succeed in adapting the patches we use we might be able to build a Debian release 5.1+d+dfsg-really5.0+f-1 and check whether the bug is fixed here. Kind regards Andreas. [1] https://github.com/pcingola/SnpEff/commit/e4f2c6b3d [2] https://salsa.debian.org/med-team/snpeff/-/tree/5.0f -- http://fam-tille.de
Bug#1029202: snippy: Error when using snpeff 5.1
Hi Pierre, given that this bug might be quite invasive to a couple of rdepends do you think it makes sense to upload some 5.1+d+dfsg+really+5.0 named copy of version 5.0? At least if upstream might need some time to respond? We might also turn your example into an autopkgtest to avoid future regressions. Kind regards Andreas. -- http://fam-tille.de
Bug#1029202: snippy: Error when using snpeff 5.1
Hi Pierre, Am Sat, Jan 21, 2023 at 10:00:32AM +0100 schrieb Pierre Gruet: > I will provide the upstream of snpeff with a minimal non-working example, as > I am unfortunately not able to understand it myself. Thanks a lot, that's actually the help I was hoping for Andreas. PS: Please add tags upstream and forwareded to have a close connection to this bug once you have contacted upstream -- http://fam-tille.de
Bug#1029202: snippy: Error when using snpeff 5.1
Package: snippy Version: 4.6.0+dfsg-1 Severity: important X-Debbugs-Cc: Pierre Gruet 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/snippyX) 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_05845.2_ASM584v2/GCF_05845.2_ASM584v2_genomic.gbff.gz gunzip GCF_05845.2_ASM584v2_genomic.gbff.gz mkdir tmp set -x snippy --cpus 4 --ram 20 --tmpdir ./tmp --reference GCF_05845.2_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-094,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
