[Debian-med-packaging] Bug#996407: diamond-aligner breaks proteinortho autopkgtest: diamond failed with code 256
Paul Gevers
elbrus at debian.org
Wed Oct 13 20:07:45 BST 2021
Source: diamond-aligner, proteinortho
Control: found -1 diamond-aligner/2.0.12-1
Control: found -1 proteinortho/6.0.31+dfsg-1
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of diamond-aligner the autopkgtest of proteinortho
fails in testing when that autopkgtest is run with the binary packages
of diamond-aligner from unstable. It passes when run with only packages
from testing. In tabular form:
pass fail
diamond-aligner from testing 2.0.12-1
proteinortho from testing 6.0.31+dfsg-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of diamond-aligner
to testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=diamond-aligner
https://ci.debian.net/data/autopkgtest/testing/amd64/p/proteinortho/15931264/log.gz
autopkgtest [02:08:50]: test run-unit-test: [-----------------------
*****************************************************************
[1;32mProteinortho[0m with PoFF version 6.0.31 - An orthology
detection tool
*****************************************************************
Detected 2 available CPU threads (adjust this with -cpus), Detected
'blastp+' version 2.11.0+
Checking input files.
Checking test/C.faa... ok
Checking test/C2.faa... ok
Checking test/E.faa... ok
Checking test/L.faa... ok
Checking test/M.faa... ok
[1;32m**Step 1**[0m
Generating indices anyway (forced).
Building database for 'test/C.faa' (109 sequences)
Building database for 'test/E.faa' (72 sequences)
Building database for 'test/L.faa' (40 sequences)
Building database for 'test/M.faa' (40 sequences)
Building database for 'test/C2.faa' (2 sequences)
[1;32m**Step 2**[0m using blastp+
Running blast analysis: 0% (0/10)
Running blast analysis: 10% (1/10)
Running blast analysis: 20% (2/10)
Running blast analysis: 30% (3/10)
Running blast analysis: 40% (4/10)
Running blast analysis: 50% (5/10)
Running blast analysis: 60% (6/10)
Running blast analysis: 70% (7/10)
Running blast analysis: 80% (8/10)
Running blast analysis: 100% (10/10)
Running blast analysis: 90% (9/10)
Running blast analysis: 100% (10/10)
[OUTPUT] -> written to test_blastp.blast-graph
[1;32m**Step 3**[0m
Clustering by similarity (Proteinortho mode) and 2 cpu core(s).
[OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv
You can extract the fasta files of each orthology group with
proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv
'test/C.faa' 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa'
(Careful: This will generate a file foreach line in the file
test_blastp.proteinortho.tsv).
[OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph
[OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary
[OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html
[OUTPUT] -> You can extract a xml version of the output using :
proteinortho2xml.pl test_blastp.proteinortho.tsv
>test_blastp.proteinortho.tsv.xml
[1;32mAll finished.[0m
*****************************************************************
[1;32mProteinortho[0m with PoFF version 6.0.31 - An orthology
detection tool
*****************************************************************
Detected 2 available CPU threads (adjust this with -cpus), Detected
'blastp+' version 2.11.0+
Checking input files.
Checking test/C.faa... test/C.faa 109 genes ok
Checking test/C2.faa... test/C2.faa 2 genes ok
Checking test/E.faa... test/E.faa 72 genes ok
Checking test/L.faa... test/L.faa 40 genes ok
Checking test/M.faa... test/M.faa 40 genes ok
[1;32m**Step 1**[0m
Generating indices anyway (forced).
Building database for 'test/C.faa' (109 sequences)
Building database for 'test/E.faa' (72 sequences)
Building database for 'test/L.faa' (40 sequences)
Building database for 'test/M.faa' (40 sequences)
Building database for 'test/C2.faa' (2 sequences)
[1;32m**Step 2**[0m using blastp+ with : synteny
Running blast analysis: 0% (0/10)
Running blast analysis: 10% (1/10)
Running blast analysis: 20% (2/10)
Running blast analysis: 30% (3/10)
Running blast analysis: 40% (4/10)
Running blast analysis: 50% (5/10)
Running blast analysis: 60% (6/10)
Running blast analysis: 70% (7/10)
Running blast analysis: 80% (8/10)
Running blast analysis: 100% (10/10)
Running blast analysis: 90% (9/10)
Running blast analysis: 100% (10/10)
[OUTPUT] -> written to test_synteny.blast-graph
[1;32m**Step 3**[0m
Clustering by similarity (Proteinortho mode) and 2 cpu core(s).
[OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv
You can extract the fasta files of each orthology group with
proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv
'test/C.faa' 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa'
(Careful: This will generate a file foreach line in the file
test_synteny.proteinortho.tsv).
Adding singles...
[OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph
[OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary
[OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html
[OUTPUT] -> You can extract a xml version of the output using :
proteinortho2xml.pl test_synteny.proteinortho.tsv
>test_synteny.proteinortho.tsv.xml
Clustering by gene-order ([1;32mPOFF mode[0m)
[1;33m[WARNING][0m proteinortho_clustering failed. I will now retry
without the OMP_PROC_BIND flag.[0m
[OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv
You can extract the fasta files of each orthology group with
proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv
'test/C.faa' 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa'
(Careful: This will generate a file foreach line in the file
test_synteny.poff.tsv).
Adding singles...
[OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
[OUTPUT] -> Summary is written to test_synteny.poff-graph.summary
[OUTPUT] -> Orthologous groups are written to test_synteny.poff.html
[OUTPUT] -> You can extract a OrthoXML (v0.3) version of the orthology
group output using :
proteinortho2xml.pl test_synteny.proteinortho.tsv
>test_synteny.proteinortho.tsv.xml
[1;32mAll finished.[0m
*****************************************************************
[1;32mProteinortho[0m with PoFF version 6.0.31 - An orthology
detection tool
*****************************************************************
Detected 2 available CPU threads (adjust this with -cpus), Detected
'diamond' version 2.0.12
Checking input files.
Checking test/C.faa... ok
Checking test/C2.faa... ok
Checking test/E.faa... ok
Checking test/L.faa... ok
Checking test/M.faa... ok
[1;32m**Step 1**[0m
Generating indices anyway (forced).
Building database for 'test/C.faa' (109 sequences)
Building database for 'test/E.faa' (72 sequences)
Building database for 'test/L.faa' (40 sequences)
Building database for 'test/M.faa' (40 sequences)
Building database for 'test/C2.faa' (2 sequences)
[1;33m
[WARNING][0m diamond failed to create a database. Most likely you don't
have write permissions in the directory of the fasta files. I will now
proceed with writing the database files to the DB/ directory in
./proteinortho_cache_test_diamond/ (-tmp).
[1;32m**Step 2**[0m using diamond
Running blast analysis: 0% (0/10)
Running blast analysis: 10% (1/10)
Running blast analysis: 20% (2/10)
Parameter-vector :
(version=6.0.31,step=0,verbose=1,debug=1,exactstep3=0,synteny=0,duplication=2,cs=3,alpha=0.5,connectivity=0.1,cpus=2,evalue=1e-05,purity=1e-07,coverage=50,identity=25,blastmode=diamond,sim=0.95,report=3,keep=0,force=1,selfblast=0,twilight=0,singles=0,clean=0,blastOptions=,nograph=0,xml=0,desc=0,tmp_path=./proteinortho_cache_test_diamond/,blastversion=2.0.12,binpath=,makedb=diamond
makedb
--in,blast=,jobs_todo=10,project=test_diamond,po_path=/usr/bin/,run_id=,threads_per_process=1,useMcl=0,freemem=-1)
[1;31m[Error][0m [1;33m diamond failed with code 256.[0m (Please
visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)
The most common sources of this error are:
- no space left on device error.
- outdated diamond, please update diamond or consider another -p algorithm.
- the databases are missing. Maybe you ran --step=1 and removed the
databases afterwards? Please rerun 'proteinortho --step=1 --force
/path/to/fastas'
- maybe the fasta files are mixed nucleotide and aminoacid sequences or
just not suited for diamond? (For example diamond only processes protein
sequences) Try 'proteinortho --step=1 --check --force
/path/to/fastas'. [0m
If you cannot solve this error, please send a report to
incoming+paulklemm-phd-proteinortho-7278443-issue- at incoming.gitlab.com
including the parameter-vector above or visit
https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for
more help.
Further more all mails to lechner at staff.uni-marburg.de are welcome
Perl exited with active threads:
1 running and unjoined
0 finished and unjoined
0 running and detached
autopkgtest [02:09:25]: test run-unit-test: -----------------------]
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