error in IQtree

Junxia Zhang

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Jul 3, 2018, 1:52:54 PM7/3/18

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Dear Dr. Minh,

I am running ModelFinder on a nt dataset (with only 1st and 2nd codon positions, 3rd codons removed) using IQtree version 1.6.3. The command line I used is as following:

iqtree -nt 30 -st DNA -s ChalCOS.5561genes.nt.1and2codons.fas -spp ChalCOS.5561genes.nt.1and2codons.partition.nex -m MF+MERGE -rcluster 10 -rcluster-max 10000 -pre 2.1_5561genes.nt.1and2codons.IQtree.MFM10 -cptime 60 -safe

But I kept getting error messages like:

.......

WARNING: Numerical underflow for lh-branch

ERROR: rategammainvar.cpp:244: double RateGammaInvar::optimizeWithEM(double): Assertion `newPInvar < 1.0' failed.

ERROR:

ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED

ERROR: *** For bug report please send to developers:

ERROR: *** Log file: 2.1_5561genes.nt.1and2codons.IQtree.MFM10.log

ERROR: *** Alignment files (if possible)

/var/spool/slurmd/job2523971/slurm_script: line 20: 4113 Aborted iqtree -nt 30 -st DNA -s ChalCOS.5561genes.nt.1and2codons.fas -spp ChalCOS.5561genes.nt.1and2codons.partition.nex -m MF+MERGE -rcluster 10 -rcluster-max 10000 -pre 2.1_5561genes.nt.1and2codons.IQtree.MFM10 -cptime 60 -safe

I put the original fasta alignment and partition files in the dropbox folder (following link) for the trouble-shooting purpose. And in this folder, you can also find the .sh file I used for submitting the job to the biocluster and the output log file.

https://www.dropbox.com/sh/197rtfocmkinhya/AAAflp6bfDJqk8r_HddJ4PQRa?dl=0

Do you know what went wrong with this analysis and what should I do to fix it?

Thank you very much!

Best,

Junxia

Junxia Zhang

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Jul 5, 2018, 3:45:33 PM7/5/18

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Hello all,

Can someone help me out with this following problem? Thank you very much!

Junxia

Minh Bui

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Jul 5, 2018, 3:47:45 PM7/5/18

to IQ-TREE, Junxia Zhang

Hi Junxia,

I just downloaded the files. Thanks for the report. Will have a look and get back later.

Cheers

Minh

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