Different results from rma and sam outputs

User Questions
1

Hello, I ran Malt on a large fastq file, and produced both sam and rma6 outputs. When I imported the sam output into Megan, I realized that the numbers were different from the rma6 output. I imported the sam file with the same mapping file as I used to build the index (the most recent one).

Can anyone explain why there is a difference and which of the two I should trust? The sam output produced many more reads and taxa:

megan sam
Reads=7,073,618 Assigned=4,321,438 (readCount) MinScore=50.0 MaxExpected=1.0 TopPercent=10.0 MinSupportPercent=0.001 MinSupport=70 disabledTaxa=13 LCA=naive mode=BlastN
taxa=50

megan rma
Reads=7,073,618 Assigned=2,747,682 (readCount) MinScore=50.0 MaxExpected=1.0 TopPercent=10.0 MinSupportPercent=0.001 MinSupport=70 disabledTaxa=13 LCA=naive mode=BlastN
taxa=31

Thanks, Hugh

2

Dear Hugh, if you could send me a link the rma6 and sam files then I will take a look at them to try to figure out what is going on.
Thanks
daniel

3

Thanks Daniel. I have sent you links. Just adding some info here in cases anyone else has some insight. Here is the command I used to generate the two outputs (sam.gz and rma6):

malt-run \
  --inFile ${DATADIR}${sample}.fastq.gz \
  --mode BlastN \
  --alignmentType SemiGlobal \
  --index /nesi/nobackup/uoo02328/references/MALT/malt_bact6k \
  --numThreads 32 \
  --output . \
  --alignments . \
  --format SAM

Cheers,
Hugh