Daa2info doesn't work (at least) since 6.8.15

#1

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
Version MEGAN Community Edition (version 6.8.18, built 21 Jul 2017)
Copyright © 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Loading MEGAN File: AA9340.erne-filter.standards.erne-filter.moranrna.pear.out.unassembled.concat.refseq_protein.daa
Total time: 0s
Peak memory: 0.0 of 111.1G

(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

#2

You need to specify

-l or --list

This isn’t very intuitive and I will remove this condition in the next release.

#3

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
Version MEGAN Community Edition (version 6.8.18, built 21 Jul 2017)
Copyright © 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Loading MEGAN File: AA9340.erne-filter.standards.erne-filter.moranrna.pear.out.unassembled.concat.refseq_protein.daa

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
HWI-ST731:125:C7T2CACXX:3:1102:14436:42362 30
HWI-ST731:125:C7T2CACXX:3:1108:19963:31560 30
HWI-ST731:125:C7T2CACXX:3:1113:8034:61097 30
HWI-ST731:125:C7T2CACXX:3:1114:4935:71310 30

/Daniel

#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.

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