I am trying to prepare some illumina fastq data for analysis with MEGAN, but MALT does not seem to detect any reads in my fastq files (which contain a total of ~9K reads).
I have built a MALT index from the genbank collection of all bacterial samples, and though there are no errors when I use malt-run, MALT standard output returns that Total reads: 0 for all files. The fastqs have been produced by samtools after some processing of the original fq files, and they look like normal fastqs to me.
Am I misinterpreting the output from MALT? Is there an error somewhere?
Commands used for malt-build and malt-run:
$MALT/malt-build -i ~/myco/genbank_bac_genomes/*.* -d index --sequenceType DNA
$MALT/malt-run -i Myco_16S_region_reads/* -d index -m BlastN -o malt_out
The output from malt-run for the first fq file, after it successfully reads in the index files:
--- ALIGNING ---:
+++++ Aligning file: Myco_16S_region_reads/Av.fq
Starting file: malt_out/Av.rma6
Finishing file: malt_out/Av.rma6
Loading MEGAN File: Av.rma6
Analyzing reads & alignments: Initialization
Total reads: 0
With hits: 0
Assig. Taxonomy: 0
MinSupport set to: 1
Applying min-support & disabled filter to Taxonomy...
Min-supp. changes: 0
Writing classification tables
Numb. Tax. classes: 0
Class. Taxonomy: 0
Analysis written to file: malt_out/Av.rma6
Num. of queries: 0
Aligned queries: 0
Num. alignments: 0
A section of one of the fastqs: