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aindj / k-SLAM

k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets
GNU General Public License v3.0
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SLAM fails when specifying --sam-file #8

Closed fbreitwieser closed 7 years ago

fbreitwieser commented 7 years ago

When I use the --sam-file option, SLAM fails.

Without it works:

$ sw/kslam/SLAM --db db/kslam/bv --output-file=test.kslam  test.fq.gz                                                                                                                                                                                                                  
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information.
When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information.
[... many of those messages, but output is generated and the command succeeds]

With --sam-file:

$sw/kslam/SLAM --db db/kslam/bv --output-file=test.kslam --sam-file=test.sam test.fq.gz
Trace back error: 5.
Segmentation fault

The SAM file has all the @SQ header line, but ends after the @PG line.

fbreitwieser commented 7 years ago

That's also linked to using a gzipped file - see #6 . When using an unzipped file it works.

aindj commented 7 years ago

k-SLAM does not work with gz files, they must be decompressed first