Analysis hangs at INITIALIZING CANDIDATE TREE SET

[zixuanxie]

Hi, Here I attach the information of my run:

IQ-TREE multicore version 2.1.2 COVID-edition for Linux 64-bit built Mar 30 2021
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    HP-Z6-G4-Workstation (AVX512, FMA3, 187 GB RAM)
Command: iqtree -s 758_aln_cat.phy -m LG+I+G4 -nt AUTO
Seed:    535420 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Mar 13 10:38:06 2023
Kernel:  AVX+FMA - auto-detect threads (44 CPU cores detected)

Reading alignment file 758_aln_cat.phy ... Phylip format detected
Alignment most likely contains protein sequences
Alignment has 3032 sequences with 117482 columns, 117205 distinct patterns
107268 parsimony-informative, 6570 singleton sites, 3644 constant sites

And here are the last few lines of the log file:

CHECKPOINT: Initial tree restored

NOTE: 174012 MB RAM (169 GB) is required!
Estimate model parameters (epsilon = 0.100)
Thoroughly optimizing +I+G parameters from 10 start values...
Init pinv, alpha: 0.000, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.609
Init pinv, alpha: 0.003, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.596
Init pinv, alpha: 0.007, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.596
Init pinv, alpha: 0.010, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.596
Init pinv, alpha: 0.014, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.595
Init pinv, alpha: 0.017, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.594
Init pinv, alpha: 0.021, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.594
Init pinv, alpha: 0.024, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.594
Init pinv, alpha: 0.028, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.593
Init pinv, alpha: 0.031, 1.000 / Estimate: 0.031, 0.748 / LogL: -58305297.592
Optimal pinv,alpha: 0.031, 0.748 / LogL: -58305297.592

Parameters optimization took 46500.554 sec
Computing ML distances based on estimated model parameters...
Computing ML distances took 139.417037 sec (of wall-clock time) 5017.326858 sec(of CPU time)
Computing RapidNJ tree took 165.753781 sec (of wall-clock time) 5572.851483 sec (of CPU time)
Log-likelihood of RapidNJ tree: -58856324.914
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 

The analysis hangs at the step of "Generating 98 parsimony trees ..." for almost 30 hours.

This analysis is consuming 178G out of 187G of the mem, but only 1 thread out of 44. I'd like to ask if it is still running or if it hangs due to some reason. If it is still running, do you know how long it might last to finish?

Thank you!

[JasmineGamblin]

Hi, I have the same situation here, so I'm interested to know whether your analysis finished after some time. Thank you!

[JasmineGamblin]

For people having the same question in the future: yes, this step takes time. The generation of 98 parsimony trees took 30 hours to finish in my case.