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

[Andreas Tille]

Hi again,

the issue is most probably caused by a broken fasta parser.  With the
following simplification of the header


 $ git diff
diff --git a/debian/tests/test_data/Acartia_tonsa.fasta b/debian/tests/test_data/Acartia_tonsa.fasta
index abcda65..011076b 100644
--- a/debian/tests/test_data/Acartia_tonsa.fasta
+++ b/debian/tests/test_data/Acartia_tonsa.fasta
@@ -1,4 +1,4 @@
->gi|441431932| Acartia tonsa copepod circovirus isolate 154_D11, complete genome
+>441431932
 ACCTCGGCAACATCCGATCATCATATGATCAATTATGACTCATCCCGCGTGGAATTATGTAGCCAATGAA
 ATCGCTCCATATTTCAAAAATTGAGTTTTCACAGTGGCCGCAATCTATAAAGCCGCGAGCGAAGCGAGCG
 GTAGGCATTTTCAGTTTGACCAAAATGCCTAGCAACGCAACAACCAACCGAGCCCGTGGGTGGTGCTTCA
diff --git a/debian/tests/test_data/Acinetobacter_phage.fasta b/debian/tests/test_data/Acinetobacter_phage.fasta
index 317a94c..591f2e0 100644
--- a/debian/tests/test_data/Acinetobacter_phage.fasta
+++ b/debian/tests/test_data/Acinetobacter_phage.fasta
@@ -1,4 +1,4 @@
->gi|28173057| Acinetobacter phage AP205, complete genome
+>28173057
 GGAGTGAACCCCGGAGGGGGTTCGCTGAAAGCCGAATCGAATTCGACTTTGCGTGATTCACATCACGTCT
 TACTCACGATACTAGTACCGCGAGTTATCTTGTGGTAATTAAAAACTACCAGGAGATAACTTTATGAAGA
 AAAGGACAAAAGCCTTGCTTCCCTATGCGGTTTTCATCATACTCAGCTTTCAACTAACATTGTTGACTGC



the test works again as expected


$ sh /usr/share/doc/kraken/run-unit-test
Added "Acartia_tonsa.fasta" to library (test_db)
Added "Acinetobacter_phage.fasta" to library (test_db)
Kraken build set to minimize disk writes.
Creating k-mer set (step 1 of 6)...
Found jellyfish v1.1.11
Hash size not specified, using '5120'
K-mer set created. [0.029s]
Skipping step 2, no database reduction requested.
Sorting k-mer set (step 3 of 6)...
K-mer set sorted. [0.030s]
Skipping step 4, GI number to seqID map now obsolete.
Creating seqID to taxID map (step 5 of 6)...
3 sequences mapped to taxa. [0.009s]
Setting LCAs in database (step 6 of 6)...
Finished processing 3 sequences                        
Database LCAs set. [0.020s]
Database construction complete. [Total: 0.105s]
2 sequences (0.00 Mbp) processed in 0.000s (983.6 Kseq/m, 94.43 Mbp/m).
  2 sequences classified (100.00%)
  0 sequences unclassified (0.00%)
  0.00  0       0       U       0       unclassified


Since we want to make sure our users will be able to work with usual
fasta files I'll open an issue upstream and leave the bug open.

Kind regards

       Andreas. 

-- 
http://fam-tille.de