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bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
http://kaiju.binf.ku.dk
GNU General Public License v3.0
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Found bad number (out of range error) #35

Closed ghost closed 7 years ago

ghost commented 7 years ago

was trying kaiju out using the kaiju_index.tgz db and ran the command: kaiju-v1.5.0-linux-x86_64-static/bin/kaiju -t .dmp -f .fmi -i firstfile.fq -j secondfile.fq -z 32

and received a whole bunch of warnings: Found bad number (out of range error) in line: 1 | all | | synonym | Found bad number (out of range error) in line: 1 | root | | scientific name | Found bad number (out of range error) in line: 2 | Bacteria | Bacteria | scientific name | Found bad number (out of range error) in line: 2 | Monera | Monera | in-part | ...

pls advise if this is expected?

Thank you.

ghost commented 7 years ago

this was followed by: terminate called after throwing an instance of 'std::out_of_range' what(): _Map_base::at Aborted

pmenzel commented 7 years ago

Hi, looks like you are passing the file names.dmp to the option -t instead of nodes.dmp (by using the shell wildcard *.dmp). Run it with: kaiju -x -z 32 -t nodes.dmp -f kaiju_db.fmi -i firstfile.fq -j secondfile.fq -o kaiju.out

ghost commented 7 years ago

thanks alot and indeed that was my error.