Both daa-meganizer and daa2rma hangs immidiately after execution

Hi,

I've been using the most recent version of MEGAN (version 6.25.3, built 15 Sep 2023) on our HPC and when trying to MEGANize my daa file, it just hangs right at the beginning and not progressing (nor exiting) until it reaches the walltime and the job terminates. This is how I generated the daa file:

diamond blastx --sensitive -q $QUERY.fasta -d $DB_DIR/ncbi/v5/nr -o $QUERY.daa -F 15 -f 100 --range-culling --top 10 -p \$NCPUS

I tried running daa-meganizer with the -v flag, but the output is still minimal and doesn't report any errors (looking at the job summary, it used ~250MB of RAM and around a minute of CPU time):

$ daa-meganizer -i $QUERY.daa -v -mdb $DB_DIR/megan/megan-map-Feb2022.db -cf contaminants.txt -t \$NCPUS
Meganizer - Prepares ('meganizes') a DIAMOND .daa file for use with MEGAN
Options:
Files
        --in: Galaxy_Flye_assembly.daa
Mode
        --longReads: false
Parameters
        --classify: true
        --minScore: 50.0
        --maxExpected: 0.01
        --minPercentIdentity: 0.0
        --topPercent: 10.0
        --minSupportPercent: 0.01
        --minSupport: 0
        --minPercentReadCover: 0.0
        --minPercentReferenceCover: 0.0
        --minReadLength: 0
        --lcaAlgorithm: naive
        --lcaCoveragePercent: 100.0
        --readAssignmentMode: readCount
        --conFile: contaminants.txt
Classification support:
        --mapDB: /project/aerc/megan/megan-map-Feb2022.db
Deprecated classification support:
        --parseTaxonNames: true
        --firstWordIsAccession: true
        --accessionTags: gb| ref|
Other:
        --threads: 12
        --cacheSize: -10000
        --propertiesFile: /export/home/s2978925/.MEGAN.def
        --verbose: true
Version   MEGAN Community Edition (version 6.25.3, built 15 Sep 2023)
Author(s) Daniel H. Huson
Copyright (C) 2023 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Java version: 20.0.2; max memory: 7.8G
=>> PBS: job killed: walltime 540048 exceeded limit 540000

I tried using daa2rma and it hangs similarly after reporting the java version:

$ daa2rma --in $QUERY.daa -mdb $DB_DIR/megan/megan-map-Feb2022.db -cf contaminants.txt -lg true -v true -t \$NCPUS -o $QUERY.rma
DAA2RMA - Computes a MEGAN .rma6 file from a DIAMOND .daa file
Options:
Input
        --in: Galaxy_Flye_assembly.daa
Output
        --out: Galaxy_Flye_assembly.rma
        --useCompression: true
Reads
        --paired: false
        --pairedSuffixLength: 0
        --pairedReadsInOneFile: false
Parameters
        --longReads: true
        --maxMatchesPerRead: 100
        --classify: true
        --minScore: 50.0
        --maxExpected: 0.01
        --minPercentIdentity: 0.0
        --topPercent: 10.0
        --minSupportPercent: 0.01
        --minSupport: 0
        --minPercentReadCover: 0.0
        --minPercentReferenceCover: 0.0
        --minReadLength: 0
        --lcaAlgorithm: longReads
        --lcaCoveragePercent: 51.0
        --readAssignmentMode: alignedBases
        --conFile: contaminants.txt
Classification support:
        --mapDB: /project/aerc/megan/megan-map-Feb2022.db
Deprecated classification support:
        --parseTaxonNames: true
        --firstWordIsAccession: true
        --accessionTags: gb| ref|
Other:
        --threads: 12
        --cacheSize: -10000
        --propertiesFile: /export/home/s2978925/.MEGAN.def
        --verbose: true
Version   MEGAN Community Edition (version 6.25.3, built 15 Sep 2023)
Author(s) Daniel H. Huson
Copyright (C) 2023 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Java version: 20.0.2; max memory: 7.8G
=>> PBS: job killed: walltime 540048 exceeded limit 540000

I'd really appreciate any help.

Thanks, Ido

husonlab / megan-ce

Both daa-meganizer and daa2rma hangs immidiately after execution #22