RAxML EPA run failed

[billzt]

SATIVA v0.9-60-g8c31962, released on 2021-01-04. Last version: https://github.com/amkozlov/sativa 
By A.Kozlov and J.Zhang, the Exelixis Lab. Based on RAxML 8.2.3 by A.Stamatakis.

SATIVA was called as follows:

./sativa-master/sativa.py -s test.fa -t test.tax -x zoo -T 3

*** STEP 1: Building the reference tree using provided alignment and taxonomic annotations ***

=> Loading taxonomy from file: test.tax ...

==> Loading reference alignment from file: test.fa ...

===> Validating taxonomy and alignment ...

====> Building a multifurcating tree from taxonomy with 5 seqs ...

=====> Building the reference alignment ...

======> Saving the outgroup for later re-rooting ...

=======> Resolving multifurcation: choosing the best topology from 1 independent RAxML runs ...

========> Calling RAxML-EPA to obtain branch labels ...

=========> Post-processing the EPA tree (re-rooting, taxonomic labeling etc.) ...

==========> Saving the reference JSON file: ./test.refjson

*** STEP 2: Searching for mislabels ***

Running the leave-one-sequence-out test...

Leave-one-out test identified 3 suspicious sequences; running final EPA test to check them...

RAxML EPA run failed, please examine the log for details:
 /home/project/sativa-master/tmp/test_1674796061776/RAxML_output.final_epa_test

In /home/project/sativa-master/tmp/test_1674796061776/RAxML_output.final_epa_test:

/home/project/sativa-master/raxml/raxmlHPC8-AVX2.PTHREADS
raxmlHPC8-AVX2.PTHREADS: treeIO.c:1232: uprootTree: Assertion `!(isTip(r->number, tr->mxtips) && isTip(q->number, tr->mxtips))' failed.
/home/project/sativa-master/raxml//run_raxml.sh: line 45: 1753114 Aborted                 (core dumped) $RAXML $@

[amkozlov]

Your dataset is too small: after pruning 3 suspicious taxa, the remaining !tree! would only contain 2 taxa. RAxML cannot work with trees with <4 taxa, but even if it could, it would still be impossible to get meaningful results in such situation.

(I know, the error message is not very descriptive)

[billzt]

Thank you !