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miwipe / ngsLCA

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ngsLCA.cpp:60: void mod_db(int*, int*, int2int&, int2char&, int2char&): Assertion `parent.count(out[i])==1' failed #32

Open itpcas-zcb opened 1 month ago

itpcas-zcb commented 1 month ago

I used sequencing data to align with Bowtie2 to the GTDB database, and then I used the gtdb_to_taxdump.py and acc2gtdb_tax.py scripts to generate name, nodes, and acc2tax files. However, I encountered an error when using ngsLCA to annotate the bam file: ngsLCA: ngsLCA.cpp:60: void mod_db(int, int, int2int&, int2char&, int2char&): Assertion `parent.count(out[i])==1' failed

miwipe commented 1 month ago

I think its a compatibility problem with the taxonomy. Could you double check the the fasta headers from GTDB are in similar formats as the ncbi fasta's. Because ngsLCA has been build around the ncbi taxonomy. I would also double check that the acc2gtdb_tax.py taxonomy files are in the exact same format as the ncbi one.