I have been creating RMA files successfully with
sam2rma, and it is handling very large datasets quite well. Thanks for providing this alongside MEGAN.
I think there may be a misspecification of the default setting for
-ram, --readAssignmentMode [string] Set the read assignment mode. Default value: readCount Legal values: readCount, readLength, alignedBases, readMagnitude
After making RMA files using the default for this flag, I noticed that total aligned bases are showing up in the plots, rather than read counts. Checking the log files, I see:
SAM2RMA6 - Computes a MEGAN RMA (.rma) file from a SAM (.sam) file that was created by DIAMOND or MALT
Deprecated classification support:
–accessionTags: gb| ref|
Version MEGAN Community Edition (version 6.19.4, built 16 Jul 2020)
The general command I’ve been using is:
sam2rma -i SAM -r READS -o OUTPUT -lg -alg longReads -t 32 -mdb DATABASE -v 2> LOG
The log file seems to indicate that the default is actually
alignedBases. I just wanted to check to see if this is the expected behavior, or if something about my SAM files caused a switch in the default?
I can certainly re-make the RMA files using
-ram readCount . However, it can take several hours to create each RMA file, and this may save some time moving forward.