I recently upgraded MEGAN to 6.8.18 to get the new hierarchical export that I asked for earlier (thank you for implementing that!). However, my exports does not work any more. I have tried with 6.8.15, 17 and 18 and none of them works; 6.8.12 does work however but doesn’t recognize the --paths option (ids are output).
This is the command and the output I get:
$ /usr/local/megan/tools/daa2info --in AA9340.erne-filter.standards.erne-filter.moranrna.pear.out.unassembled.concat.refseq_protein.daa -r2c SEED --names
(In 6.8.12 there was a message about loading a file, then it got started with the export.)
I also tried with other export categories, besides SEED.
I tried rerunning diamond (0.8.24) as well as the meganizing if this was a file format issue, but to no avail.
/Daniel
Daniel
August 7, 2017, 4:20pm
2
You need to specify
-l or --list
This isn’t very intuitive and I will remove this condition in the next release.
Not very intuitive, I agree ;-).
However, I don’t get the --paths option to work. The program outputs ids instead:
$ /usr/local/megan/tools/daa2info --in AA9340.erne-filter.standards.erne-filter.moranrna.pear.out.unassembled.concat.refseq_protein.daa -r2c SEED --list --paths |head
Number of reads: 1,158,976
Alignment mode: BLASTX
Is meganized: true
Classifications: EGGNOG INTERPRO2GO SEED Taxonomy
Reads to class for ‘SEED’:
HWI-ST731:125:C7T2CACXX:3:2108:8599:60906 29
/Daniel
Daniel
September 5, 2017, 8:57pm
4
Hi Daniel, this is not a bug, the option “paths” was not implemented for functional classifications. However, I have now implemented this feature and it will be available in the next release.