IQTREE PMSF crash

[erikrikarddaniel]

Hi,

I'm trying PMSF for the first time, but IQTREE crashes (see attached log file for details). Here are the last lines:

===> COMPUTING SITE FREQUENCY MODEL BASED ON TREE FILE nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.iqtree.MFP.treefile
Model LG+C20+I+G is alias for LG+POISSON+G+FMIX{C20pi1:1:0.0559910600,C20pi2:1:0.0514824870,C20pi3:1:0.0812922124,C20pi4:1:0.0721976867,C20pi5:1:0.0556718858,C20pi6:1:0.0331003080,C20pi7:1:0.0589501763,C20pi8:1:0.0263756889,C20pi9:1:0.0307584220,C20pi10:1:0.0376701125,C20pi11:1:0.0303058290,C20pi12:1:0.0808775576,C20pi13:1:0.0263349134,C20pi14:1:0.0579101455,C20pi15:1:0.0371248064,C20pi16:1:0.0586867766,C20pi17:1:0.0561479138,C20pi18:1:0.0349810886,C20pi19:1:0.0544937394,C20pi20:1:0.0596471901}+I+G
NOTE: 12848 MB RAM is required!
Measuring multi-threading efficiency up to 24 CPU cores
ERROR: phylotreepars.cpp:63: void PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*): Assertion `!aln->ordered_pattern.empty()' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 1   funcAbort()
ERROR: 2   ()   
ERROR: 3   pthread_kill()
ERROR: 4   gsignal()
ERROR: 5   abort()
ERROR: 6   ()   
ERROR: 7   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 8   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 9   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 10   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 11   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 12   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 13   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 14   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 15   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 16   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 17   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 18   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 19   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 20   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 21   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 22   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 23   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 24   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 25   PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*)
ERROR: 26   PhyloTree::computeParsimonyBranchFast(PhyloNeighbor*, PhyloNode*, int*)
ERROR: 27   PhyloTree::setParsimonyBranchLengths()
ERROR: 28   PhyloTree::wrapperFixNegativeBranch(bool)
ERROR: 29   PhyloTree::testNumThreads()
ERROR: 30   PhyloTree::ensureNumberOfThreadsIsSet(Params*)
ERROR: 31   computeSiteFrequencyModel(Params&, Alignment*)
ERROR: 32   runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&)
ERROR: 33   runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 34   main()
ERROR: 35   ()   
ERROR: 36   __libc_start_main()
ERROR: 37   ()   
ERROR: 
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.iqtree.PMSF.LGC20IG.log
ERROR: ***    Alignment files (if possible)

I start with an alignment I used for a regular run of IQTREE and the tree produced. I've tried both "LG+C20+I+G" and "LG+C20+I+R10" (LG+I+R10 was found in the first round).

IQTREE 3.0.1 installed by Conda. The command was:

iqtree \
  -s nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.alnfaa \
  -B 1000 -nt AUTO -m LG+C20+I+G \
  -ft nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.iqtree.MFP.treefile \
  --prefix nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.iqtree.PMSF.LGC20IG

I attach also the alignment and treefile (both with appended .txt suffixes to allow upload).

nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.iqtree.PMSF.LGC20IG.log
nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.alnfaa.txt
nrdab_consistent_200_0.75_NrdAB_concat.BLOSUM30.bmge.short_names.iqtree.MFP.treefile.txt

Thanks for an otherwise fantastic piece of software!

/D