Generating a taxonomic classification text file rma file on command line?

User Questions
1

Hey All

I have many rma files, and instead of generating an output taxonomy text file using GUI Megan, I am interested in a more of an automated version. I understand “Blast2LCA” generates a taxonomic file. Is it possible to do so from rma file?
I am using MEGAN Community Edition (version 6.19.6).

2

Yes, please use the command line program rma2info to extract classifications etc from rma files.

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3

Thank you for replying! I am using rma2info, and its generating an empty output file.

Code used-
$/home/j/jigyasa-arora/megan/tools/rma2info -i swissprot-matches-2-rumen_contigs.rma -o output.txt

The rma file -
-rw-r–r-- 1 jigyasa-arora 3.3G Aug 5 18:04 swissprot-matches-2-rumen_contigs.rma

MEGAN version I am using-Version MEGAN Community Edition (version 6.19.6, built 30 Jul 2020)

Additionally, I am using swissprot database for DIAMOND blast, and “megan-map-Jul2020-2.db” mapping file. But I don’t get an virus taxonomy in it (virus contigs exists, as its based on recently published data). Any suggestions on if I am using the wrong mapping file or not?

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4

You need to specify what you want rma2info to do, using one of the following options (use -h to get full help listing):

-l, --list                           List general info about file. Default value: false.
-m, --listMore                       List more info about file (if meganized). Default value: false.
-c2c, --class2count [string(s)]      List class to count for named classification(s) (Possible values: EC EGGNOG GTDB INTERPRO2GO KEGG SEED Taxonomy). 
-r2c, --read2class [string(s)]       List read to class assignments for named classification(s) (Possible values: EC EGGNOG GTDB INTERPRO2GO KEGG SEED Taxonomy). 
-n, --names                          Report class names rather than class Id numbers. Default value: false.
-p, --paths                          Report class paths rather than class Id numbers. Default value: false.
-r, --ranks                          When reporting taxonomy, report taxonomic rank using single letter (K for Kingdom, P for Phylum etc). Default value: false.
-mro, --majorRanksOnly               Only use major taxonomic ranks. Default value: false.
-bo, --bacteriaOnly                  Only report bacterial reads and counts in taxonomic report. Default value: false.
-vo, --virusOnly                     Only report viral reads and counts in taxonomic report. Default value: false.
-u, --ignoreUnassigned               Don't report on reads that are unassigned. Default value: true.
-es, --extractSummaryFile [string]   Output a MEGAN summary file (contains all classifications, but no reads or alignments).

I’m not sure why you are not seeing any virus hits. The regular mapping database is optimized for use with the NCBI-nr database. For Swissprot, please try using the extended mapping database https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-map-Jul2020-2-X.db.zip.
Please let me know whether this fixes the problem.

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5

Hey Daniel

Thank you for replying! I tried mapping to the extended mapping database-https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-map-Jul2020-2-X.db.zip.
I don’t get any assigned reads now.
The rma file is 3.3Gb is size, but when I upload it to MEGAN GUI version, all reads are unassigned.
rma2info command on command line version generates an empty file too.

Please let me know if you need any specific file to reproduce my analysis.
I tried uploading the meganized daa file, but it doesn’t load completely.

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6

I’m having the same problem.

7

If you can give me access to a small file that exhibits the problem then I’d be happy to look at it (but I will be for the next ten days…)