[Debian-med-packaging] Bug#889623: kraken: failing autopkgtest, possibly broken package

[Andreas Tille]

Hi,

since upstream claimed to have fixed a bug unrelated to this test case I
meanwhile uploaded kraken 1.1.  To simplify fixing the issue here is the
output of the autopkgtest script on a local machine:


$ sh /usr/share/doc/kraken/run-unit-test
scan_fasta_file.pl: unable to determine taxonomy ID for sequence gi|441431932|
scan_fasta_file.pl: unable to determine taxonomy ID for sequence gi|28173057|
Kraken build set to minimize disk writes.
Creating k-mer set (step 1 of 6)...
Found jellyfish v1.1.11
kmer_estimator: malformed fasta file - expected header char > not found
Hash size not specified, using '2560'
terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError'
  what():  Empty input file '/dev/fd/0': Success
/usr/lib/kraken/build_kraken_db.sh: Zeile 96:  4909 Fertig                  find library/ -name '*.fna' -print0
      4910                       | xargs -0 cat
      4911 Abgebrochen             | jellyfish1 count -m $KRAKEN_KMER_LEN -s $KRAKEN_HASH_SIZE -C -t $KRAKEN_THREAD_CT -o database /dev/fd/0
kraken: database ("./test_db") does not contain necessary file database.kdb
kraken-report: database ("./test_db") does not contain necessary file database.kdb


It would be really great if somebody could have a look

      Andreas.


-- 
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