#14 Problem running taxtree

[Antonio Nhani Jr]

Hi,
I used
taxtree.sh names.dmp nodes.dmp merged.dmp tree.taxtree.gz
and got
Exception in thread "main" java.lang.AssertionError: No level found for subcohort; line=[32519, 186634, subcohort, | 10|1 | 1 | 1 | 2 | 1 | 0 | 0 | |]
at tax.TaxTree.getNodes(TaxTree.java:543)
at tax.TaxTree.<init>(TaxTree.java:223)
at tax.TaxTree.<init>(TaxTree.java:213)
at tax.TaxTree.main(TaxTree.java:57)</init></init>

running in
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b31)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b31, mixed mode)

uname -a
Linux 2.6.32-573.7.1.el6.x86_64

Coulkd you help?

Best,

Antonio

[Antonio Nhani Jr]

Update:
running with -da option:

taxtree.sh -da names.dmp nodes.dmp merged.dmp tree.taxtree.gz
java -da -Xmx54807m -Xms54807m -cp /home/m322745/bin/bbmap/current/ tax.TaxTree -da names.dmp nodes.dmp merged.dmp tree.taxtree.gz
Found 1 unknown taxonomic levels:
Counted children.
Percolated 9 rounds to fixpoint.
Assigning strains.
Percolated 2 rounds to fixpoint.
Assigned levels to 173224 unranked nodes.
Percolated 2 rounds to fixpoint.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
at tax.TaxTree.<init>(TaxTree.java:253)
at tax.TaxTree.<init>(TaxTree.java:213)
at tax.TaxTree.main(TaxTree.java:57)</init></init>

[Brian Bushnell]

The problem is that NCBI added a new taxonomic level, "subcohort", which they did not previously use (this happens occasionally). I just put in support for "subcohort" in the code and BBTools 38.36 can handle the lastest taxonomy data fine; I'll release it in a little while.

[Brian Bushnell]

The new version is available now.