Package: diamond-aligner
Version: 0.9.31-1
Severity: serious
Tags: ftbfs
Control: affects -1 src:proteinortho
https://ci.debian.net/data/autopkgtest/testing/arm64/p/proteinortho/4965864/log.gz
https://buildd.debian.org/status/package.php?p=proteinortho=sid
...
make -j4 test
make[1]: Entering directory '/<>'
[TEST] Clean up all test files...
[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present
are skipped)
[TEST] Clean up all test files...
[1/12] -p=blastp+ test: passed
[2/12] -p=blastp+ synteny (PoFF) test: tput: No value for $TERM and no -T
specified
[STDERR] Error: wrong fromat... Please make sure you only provide *.blast-graph
or *.proteinortho-graph files as input...
Died at .//src/BUILD/Linux_aarch64/proteinortho_summary.pl line 117, <$FH> line
2.
USAGE: proteinortho2html.pl ( ...)
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.
passed
[3/12] -p=diamond test:
Parameter-vector :
(version=6.0.15,step=0,verbose=0,debug=1,exactstep3=0,synteny=0,duplication=2,cs=3,alpha=0.5,connectivity=0.1,cpus=4,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=.//src/BUILD/Linux_aarch64,run_id=,threads_per_process=1,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- outdated diamond, please update diamond or consider another -p algorithm.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-iss...@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 lech...@staff.uni-marburg.de are welcome)
Perl exited with active threads:
3 running and unjoined
0 finished and unjoined
0 running and detached
Error, could not open file test_diamond.proteinortho.tsv: No such file or
directory at ./src/chk_test.pl line 6.
make[1]: *** [Makefile:253: test_step2] Error 2
