I’m running a metabarocoding analysis and am trying to build a reference index with with malt-build (0.41) using the megan-nucl-Jul2020.db mapping file, but I get a java.lang.NullPointerException and thus the index is not correctly built (all taxonomy assignments are reported as No hits in Megan). The same happens with an older megan-map-Oct2019.db, but not with the nucl_acc2tax-Jul2019.abin. So I guess it has something to do with transforming to SQLite database and malt-build not reading the mapping .db files.
Going through other reports/crashes on the Megan CE pages I found a similar report from January this year, regarding Aadder-build java.lang.NullPointerException with the new .db file, where it was pointed out that aadder-build (at that time) still required .abin mapping files. I think this was sorted in the next Megan release for aadder-build.
Probably this is a similar issue. Next to using the nucl_acc2tax-Jul2019.abin, which is a bit outdated, can we expect a new version of malt that will be compatibly with .db files.
Going through old posts on the website I found a workaround but it requires quite a lot of memory. I downloaded the mapping file from ncbi (ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/) and prepared a text acc2tax mapping file from it with this command:
gunzip nucl_gb.accession2taxid.gz|cut -f1,3 |gzip >nucl_gb.accession2taxid.map.gz.
As I had access to a suitable server with sufficient memory I was able to build the index. However, I am still not 100% sure this is a correct path?