IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT? - version 1.6.6

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Sarah Lock

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Apr 22, 2020, 6:05:39 AM4/22/20
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Hello, 

I was wondering if anyone could help me. I am running a partition model using the following code.

iqtree -s paths_cut-gb.seq -sp partition_list.txt -m TESTMERGE -bb 5000 -nt AUTO -alrt 1000 -redo


However I keep getting the following error (end of log file):


ERROR: STACK TRACE FOR DEBUGGING:

ERROR: 1   funcAbort()

ERROR: 2   ()

ERROR: 3   pllPartitionsValidate()

ERROR: 4   IQTree::initializePLL(Params&)

ERROR: 5   startTreeReconstruction(Params&, IQTree*&, ModelCheckpoint&)

ERROR: 6   runPhyloAnalysis(Params&, Checkpoint*)

ERROR: 7   main()

ERROR: 8   __libc_start_main()

ERROR: 

ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

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

ERROR: ***    Log file: partition_list.txt.log

ERROR: ***    Alignment files (if possible)


Begining of log file: 


IQ-TREE multicore version 1.6.6 for Linux 64-bit built Feb 19 2019

Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,

Heiko Schmidt, Dominik Schrempf, Michael Woodhams.


Host:    login1.pri.viking.alces.network (AVX512, FMA3, 187 GB RAM)

Command: iqtree -s paths_cut-gb.seq -sp partition_list.txt -m TESTMERGE -bb 5000 -nt AUTO -alrt 1000 -redo

Seed:    776800 (Using SPRNG - Scalable Parallel Random Number Generator)

Time:    Wed Apr 22 10:33:40 2020

Kernel:  AVX+FMA - auto-detect threads (40 CPU cores detected)


Reading partition model file partition_list.txt ...

Reading alignment file paths_cut-gb.seq ... Fasta format detected

Alignment most likely contains DNA/RNA sequences



I have run this before with different sequences and not had any problems, I have checked the alignment and partition files and can't seem to find any problems. I have attached both these and the log file below. 


Thank you!


partition_list.txt
partition_list.txt.log
paths_cut-gb.seq

Minh Bui

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Apr 27, 2020, 11:14:48 PM4/27/20
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Hi Sarah,

There is something wrong in the PLL library used internally in IQ-TREE to compute a parsimony tree. Therefore, please add option -t PARS to switch to IQ-TREE own kernel for this. This PLL version 1 is not maintained anymore, so I can’t notify the developers.

Thanks
Minh

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<partition_list.txt><partition_list.txt.log><paths_cut-gb.seq>

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