Aadder database SQL and IndexOutOfBounds Exceptions

Bug Reports
1

Hello,

I am trying to build an AADDer database with the new mapping file megan-map-Jul2020-2.db and megan version 6_20_14 tools aadder-build script, but I get the error
java.sql.SQLException: java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0

I ran megan_6_20_14/tools/aadder-build -igff refseq/bacteria_archea_homo_20181122/raw/ -d databases/aadder/ -mdb megan-map/megan-map-Jul2020-2.db -ex -v using Ubuntu 18.04.4 LTS.

and the full error is

AAdderBuild - Build the index for AAdd
Options:
Input Output
        --inputGFF: refseq/bacteria_archea_homo_20181122/raw/
        --index: databases/aadder/
Classification mapping:
        --mapDB: megan-map-Jul2020-2.db
Deprecated classification mapping options:
Other:
        --extraStrict: true
        --verbose: true
Version   MEGAN Community Edition (version 6.20.14, built 11 Nov 2020)
Author(s) Daniel H. Huson
Copyright (C) 2020 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Looking for GFF3 files in directory: refseq/bacteria_archea_homo_20181122/raw
Found: 31,276
Caught:
java.sql.SQLException: java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
        at megan/megan.accessiondb.AccessAccessionMappingDatabase.getSize(AccessAccessionMappingDatabase.java:184)
        at megan/megan.tools.AAdderBuild.setupCreator(AAdderBuild.java:155)
        at megan/megan.tools.AAdderBuild.run(AAdderBuild.java:117)
        at megan/megan.tools.AAdderBuild.main(AAdderBuild.java:63)
Caused by: java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0
        at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
        at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
        at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
        at java.base/java.util.Objects.checkIndex(Objects.java:373)
        at java.base/java.util.ArrayList.get(ArrayList.java:426)
        at megan/megan.accessiondb.AccessAccessionMappingDatabase.getSize(AccessAccessionMappingDatabase.java:182)
        ... 3 more

Is AADDer updated to take the new mapping file, or is there possibly something wrong with the file I downloaded?

Thank you,
Irina

2

Thanks for the bug report. I have found and fixed the problem and will upload a new release today.