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Old 07-25-2017, 09:25 AM   #1
Junior Member
Location: Southwest US

Join Date: Jul 2017
Posts: 1
Default MALT/MEGAN question

Hello all,

I'm trying to use MALT/MEGAN for the first time through ubuntu. I have a FASTA file of some shotgun microbial sequences that I converted from an Illumina HiSeq FASTQ output and I'm trying it to run these through the examples in the MALT manual locally on my machine. MALT is properly installed universally, as is MEGAN.

Here's my command line for malt-build:

malt-build -i ./Viral_Reference/viral.1.1.genomic.fna.gz -d index -a2taxonomy ./nucl_acc2tax-May2017.abin -s DNA

I then did the following:
malt-run -i 05C_test.fasta -d ./index -m BlastN -o .

it says it's coming back with 10,440 queries, 11 aligned queries and 22 num. alignments. This all seemed to work fine and produced the necessary tree and mapping files.

after doing this in the command line:
MEGAN -g -f ./05C_test.rma6 -E

I'm getting the following:

Executing: load treeFile='ncbi.tre';
Loading mapping file:
Reading file: 1266115
Loading taxonomy file: ncbi.tre
Reading file: ncbi.tre: 1266115
Executing: open file='./05C_test.rma6';
Alert - Open file failed: File has unknown type: ./05C_test.rma6

It seems this is an issue with the rm6 output format. My java is up to date-1.8.0_131. I don't think it is an input problem either.

One additional question:
I can't seem to use -f to get an output of Tab or Text. it's giving me a kickback the -f and --format are not functional. is this a problem other users have experienced?

Thank you very much,

UPDATE 7/26/17:
Looks like this is an issue with Ubuntu version of MEGAN not being compatible with .rma6 extension files. I opened the file just fine on the Windows 64bit version of MEGAN. I've alerted the developers about this issue.

Anyone else using MALT here?

Last edited by AncientGenomes; 07-26-2017 at 10:27 AM. Reason: Compatibility issue identified
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Old 11-03-2017, 04:06 PM   #2
Junior Member
Location: Mexico

Join Date: Nov 2017
Posts: 1
Default different problem

Im using MALT for the first time too and I have some doubts about building the index.
My command line for malt-build is :

malt-build -i /mnt/Archives/BLAST_databases/nt/*.* -d Index -a2taxonomy /mnt/Cromosoma/mavila/mbravo/malt/data/gi_taxid-March2015X.bin --sequenceType DNA

It creates the following files:
index0.idx ref.idx table0.db table0.idx

but they`re empty.

I will appreciate any comment.
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Old 03-16-2018, 07:04 AM   #3
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Location: Copenhagen, Denmark

Join Date: Mar 2018
Posts: 1


@mbravo , maybe the files are empty because you are using a gi_taxid table instead of an acc_taxid table in the parameter "-a2taxonomy /mnt/Cromosoma/mavila/mbravo/malt/data/gi_taxid-March2015X.bin".
Sama is offline   Reply With Quote

blast, malt, malt-build, malt-run, megan

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