[Debian-med-packaging] Bug#958515: diamond-aligner breaks proteinortho autopkgtest on arm64: Error: wrong fromat
Paul Gevers
elbrus at debian.org
Thu Apr 23 10:08:42 BST 2020
Source: diamond-aligner, proteinortho
Control: found -1 diamond-aligner/0.9.31-1
Control: found -1 proteinortho/6.0.14+dfsg-1
Severity: serious
Tags: sid bullseye
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 on arm64 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 0.9.31-1
proteinortho from testing 6.0.14+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/arm64/p/proteinortho/5105579/log.gz
autopkgtest [14:23:33]: test run-unit-test: [-----------------------
*****************************************************************
[1;32mProteinortho[0m with PoFF version 6.0.14 - An orthology
detection tool
*****************************************************************
Detected 32 available CPU threads (adjust this with -cpus), Detected
'blastp+' version 2.9.0+
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: 100% (10/10)
Running blast analysis: 80% (8/10)
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: 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) using up to 96343.5 MB of
memory (75% of total memory) and 32 cpu core(s). Adjust this behaviour
with the -mem option.
Reading test_blastp.blast-graph
5 species
113 paired proteins
148 bidirectional edges
Clustering: 85.84%
Clustering: 89.38%
Clustering: 93.81%
Clustering: 95.58%
Clustering: 100.00%
Done
[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
[1;32mAll finished.[0m
*****************************************************************
[1;32mProteinortho[0m with PoFF version 6.0.14 - An orthology
detection tool
*****************************************************************
Detected 32 available CPU threads (adjust this with -cpus), Detected
'blastp+' version 2.9.0+
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: 100% (10/10)
Running blast analysis: 80% (8/10)
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: 90% (9/10)
Running blast analysis: 60% (6/10)
Running blast analysis: 70% (7/10)
Running blast analysis: 100% (10/10)
[OUTPUT] -> written to test_synteny.blast-graph
[1;32m**Step 3**[0m
Clustering by similarity (Proteinortho mode) using up to 96343.5 MB of
memory (75% of total memory) and 32 cpu core(s). Adjust this behaviour
with the -mem option.
Reading test_synteny.blast-graph
5 species
113 paired proteins
148 bidirectional edges
Clustering: 85.84%
Clustering: 89.38%
Clustering: 93.81%
Clustering: 95.58%
Clustering: 100.00%
Done
[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
Clustering by gene-order ([1;32mPOFF mode[0m)
Reading test_synteny.ffadj-graph
5 species
106 paired proteins
105 bidirectional edges
Clustering: 17.92%
Clustering: 61.32%
Clustering: 81.13%
Clustering: 83.02%
Clustering: 84.91%
Clustering: 86.79%
Clustering: 88.68%
Clustering: 90.57%
Clustering: 92.45%
Clustering: 98.11%
Clustering: 100.00%
Done
[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 $TERM and no -T specified
[STDERR] Error: wrong fromat... Please make sure you only provide
*.blast-graph or *.proteinortho-graph files as input...
Died at /usr/bin//proteinortho_summary.pl line 117, <$FH> line 2.
[OUTPUT] -> Summary is written to test_synteny.poff-graph.summary
USAGE: proteinortho2html.pl <myproject.proteinortho> (<fasta1> <fasta2> ...)
the first argument points to the proteinortho output (tsv)-file. Any
further (optional) files should be fasta files, for conversion of the
identifier to a proper gene name/ describtion. The HTML output is
printed to stdout, use '>' to write the html output to a file.
[OUTPUT] -> Orthologous groups are written to test_synteny.poff.html
[1;32mAll finished.[0m
*****************************************************************
[1;32mProteinortho[0m with PoFF version 6.0.14 - An orthology
detection tool
*****************************************************************
Detected 32 available CPU threads (adjust this with -cpus), Detected
'diamond' version 0.9.31
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 diamond
Running blast analysis: 0% (0/10)
Parameter-vector :
(version=6.0.14,step=0,verbose=1,debug=1,exactstep3=0,synteny=0,duplication=2,cs=3,alpha=0.5,connectivity=0.1,cpus=32,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=unknown,binpath=,makedb=diamond
makedb
--in,blast=,jobs_todo=10,project=test_diamond,po_path=/usr/bin/,run_id=,threads_per_process=3,useMcl=0,freemem=-1)
[1;31m[Error][0m [1;33m diamond failed.
The most likely errorsources of this 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:
31 running and unjoined
0 finished and unjoined
0 running and detached
autopkgtest [14:23:55]: test run-unit-test: -----------------------]
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