I am trying to classify some reads using a custom reference package of Salmonella 16S sequences. Everything goes fine until I try to classify the sequences and I get:
Uncaught exception: Failure("tax_id 913074 is not represented on the classification tree. this suggests the placefile was classified with an old version of the reference package")
Fatal error: exception Failure("tax_id 913074 is not represented on the classification tree. this suggests the placefile was classified with an old version of the reference package")
I know this is not an older version as it was built last week. The problem seems to be that 913074 is a parent of several sequences that I have (and thus does not have a sequence itself in the reference alignment) but it does not seem to be able to find it. If I randomly change the taxid of a sequence in the Seq_info file to 913074 it works. Thus it appears there is maybe a bug that is having difficulty finding this node just in the taxonomy file alone. I have attached the jplace file I am trying to classify along with the reference package. The commands I ran are:
From Conor Meehan--
I am trying to classify some reads using a custom reference package of Salmonella 16S sequences. Everything goes fine until I try to classify the sequences and I get: Uncaught exception: Failure("tax_id 913074 is not represented on the classification tree. this suggests the placefile was classified with an old version of the reference package")
Fatal error: exception Failure("tax_id 913074 is not represented on the classification tree. this suggests the placefile was classified with an old version of the reference package")
I know this is not an older version as it was built last week. The problem seems to be that 913074 is a parent of several sequences that I have (and thus does not have a sequence itself in the reference alignment) but it does not seem to be able to find it. If I randomly change the taxid of a sequence in the Seq_info file to 913074 it works. Thus it appears there is maybe a bug that is having difficulty finding this node just in the taxonomy file alone. I have attached the jplace file I am trying to classify along with the reference package. The commands I ran are:
rppr prep_db --sqlite MURB092_S83_L001_classify.db -c salmonella.refpkg/;
guppy classify --sqlite MURB092_S83_L001_classify.db --mrca-class -c salmonella.refpkg MURB092_S83_L001_salmonellaReads_pynast_aligned.jplace;