Running partitioned analysis with mixed data

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Matt Girard

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Jun 12, 2018, 12:19:16 PM6/12/18
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Hello,

I am attempting to run a partitioned analysis with mixed data on version 1.6 of IQTree but for some reason IQTree keeps entering an unending loop when loading the molecular sub-alignment. I am using two sub-alignments in .phy format, one for morphological and one for molecular data, and a single .nex file (example.nex) that has all the partitions with sub-alignment file designations as well as models designated for each partition. When executing IQTree, using:

iqtree -spp example.nex

the software loads the morphological alignment but then continuously loops over loading the molecular alignment, repeatedly calculating gap/ambiguity, p-value, and composition values for the molecular alignment but never moving past this to load the partitions. I have tried different flags (-spp, -sp, -q) when calling the file but have the same issue. Trying to figure out if there was something wrong with my alignment or partition file, I started IQTree with just molecular alignment. In that case the software performed without this loop and began the analyses. Has this been mentioned previously with 1.6? I have tried with multiple operating systems and remade all my files but still have the same outcome. 

Thank you for any assistance you can offer,

Matt

Minh Bui

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Jun 13, 2018, 9:12:32 AM6/13/18
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Hi Matt,

Though I suspect there is something wrong with your input file, it’s not possible to answer your question without looking at the input file and the log file. Thus, can you send me these files via my personal email?

Thanks
Minh

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Matt Girard

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Jun 14, 2018, 12:19:35 PM6/14/18
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Hi Minh,

After sending you an email yesterday with the files you asked for, the loop finally ended and progressed to the next phase of the analysis. It looped the same number of times as partitions I have specified in the input. While progress has been made, I now am receiving a new error: 

Log-likelihood of BIONJ tree: -3903526.137

--------------------------------------------------------------------

|             INITIALIZING CANDIDATE TREE SET                      |

--------------------------------------------------------------------

Generating 98 parsimony trees... ERROR: Tree file does not start with an opening-bracket '(' (line 1 column 1)


I have checked the tree files that IQTree has generated and there do not seem to be any issues with opening brackets or mismatched brackets. I saw this error was mentioned in a previous post from September, but it was not clear to me if a solution had be found. 


Thank you as always for any assistance you can provide,


Matt

Minh Bui

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Jun 14, 2018, 9:28:33 PM6/14/18
to IQ-TREE, Matt Girard
Hi Matt, 

I see, indeed I suspected the same after looking at your partition file. To avoid heavy loading, you can change your partition file from:

#nexus
begin sets;
charset Subset1 = dna.phy:…;
charset Subset760 = dna.phy:415534-416203\3;
charset Subset761 = morph.phy:1-275;

To

#nexus
begin sets;
charset Subset1 = …;
charset Subset760 = 415534-416203\3;
charset Subset761 = morph.phy:1-275;

Meaning that just delete dna.phy, and then provide it via -s dna.phy in the command line. That way, this file will be loaded only once.

Regarding

Generating 98 parsimony trees... ERROR: Tree file does not start with an opening-bracket '(' (line 1 column 1)

Please re-run with option -redo, which will completely redo the analysis. Let me know if that works.

Cheers
Minh
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