Use of uninitialized value in numeric comparison in kreport

[papanikos]

Hello,

I used NCBi's Refseq 16S sequences to build and test an index with centrifuge (default options). I am using the release 1.0.3 installed via conda.

I am getting this error when running the centrifuge-kreport on centrifuge output.

$ centrifuge-kreport -x refseq_16S centrifuge.out > centrifuge.kreport
Loading taxonomy ...
Loading names file ...
Loading nodes file ...
Use of uninitialized value in printf at /exports/sasc/nikos/src/biowdl/pipeline-template/conda_envs/centrifuge/bin/centrifuge-kreport line 133, <> line 324039.
Use of uninitialized value in printf at /exports/sasc/nikos/src/biowdl/pipeline-template/conda_envs/centrifuge/bin/centrifuge-kreport line 133, <> line 324039.
Use of uninitialized value in numeric comparison (<=>) at conda_envs/centrifuge/bin/centrifuge-kreport line 136, <> line 324039.
Use of uninitialized value in printf at /conda_envs/centrifuge/bin/centrifuge-kreport line 133, <> line 324039.
<truncated output>

The offending line of the centrifuge input looks like this (first column is to display the line number from less )

324039 MISEQ:94:000000000-BPK8Y:1:2119:9649:25206      NR_113345.1     1283    72965   0       393     463     1

The name column of the centrifuge_report.tsv also seems off.

$ head -n5 centrifuge_report.tsv
name    taxID   taxRank genomeSize      numReads        numUniqueReads  abundance
136     136     order   1482    1       0       0.0
286     286     genus   2072    124     119     0.0
287     287     species 6014    14208   0       0.0151014
352     352     genus   0       3       0       0.0

centrifuge-inspect with options -n and -s on the index seems OK. Any help much appreciated!

[mourisl]

We have updated centrifuge-kreport several times after 1.0.3, can you try the newer version? Thanks.