Please help me resolve this issue

[Abaranjitha Muniyasamy]

INFO     | 2022-05-22 20:02:03,150 | Setting phylogeny program to 'phyml'
INFO     | 2022-05-22 20:02:03,150 | Program path is here /scrfs/storage/amuniyas/home/Fish_Genome_Project/Phylogenetics/Partition_Finder/partitionfinder-2.1.1/programs
INFO     | 2022-05-22 20:02:03,152 | Setting working folder to: '/home/amuniyas/Fish_Genome_Project/Phylogenetics/Partition_Finder/aic_cott'
INFO     | 2022-05-22 20:02:03,154 | Loading configuration at './partition_finder.cfg'
INFO     | 2022-05-22 20:02:03,169 | Setting 'alignment' to 'cott_concatenated_alignment.phy'
INFO     | 2022-05-22 20:02:03,170 | Setting 'branchlengths' to 'unlinked'
INFO     | 2022-05-22 20:02:03,171 | You set 'models' to: all
INFO     | 2022-05-22 20:02:03,285 | This analysis will use the following 56 models of molecular evolution
INFO     | 2022-05-22 20:02:03,286 | JC, K80, TRNEF, K81, TVMEF, TIMEF, SYM, F81, HKY, TRN, K81UF, TVM, TIM, GTR, JC+G, K80+G, TRNEF+G, K81+G, TVMEF+G, TIMEF+G, SYM+G, F81+G, HKY+G, TRN+G, K81UF+G, TVM+G, TIM+G, GTR+G, JC+I, K80+I, TRNEF+I, K81+I, TVMEF+I, TIMEF+I, SYM+I, F81+I, HKY+I, TRN+I, K81UF+I, TVM+I, TIM+I, GTR+I, JC+I+G, K80+I+G, TRNEF+I+G, K81+I+G, TVMEF+I+G, TIMEF+I+G, SYM+I+G, F81+I+G, HKY+I+G, TRN+I+G, K81UF+I+G, TVM+I+G, TIM+I+G, GTR+I+G
INFO     | 2022-05-22 20:02:03,287 | Setting 'model_selection' to 'aic'
INFO     | 2022-05-22 20:02:03,308 | Setting 'search' to 'greedy'
INFO     | 2022-05-22 20:02:03,309 | ------------------------ BEGINNING NEW RUN -------------------------------
INFO     | 2022-05-22 20:02:03,310 | Looking for alignment file './cott_concatenated_alignment.phy'...
INFO     | 2022-05-22 20:02:03,311 | Using 32 cpus
INFO     | 2022-05-22 20:02:03,312 | Beginning Analysis
INFO     | 2022-05-22 20:02:03,359 | Reading alignment file './cott_concatenated_alignment.phy'
WARNING  | 2022-05-22 20:02:03,394 | These columns are missing from the block definitions: 4552, 4555, 4558, 4561, 4564, 4567, 4570, 4573, 4576, 4579, 4582, 4585, 4588, 4591, 4594, 4597, 4600, 4603, 4606, 4609, 4612, 4615, 4618, 4621, 4624, 4627, 4630, 4633, 4636, 4639, 4642, 4645, 4648, 4651, 4654, 4657, 4660, 4663, 4666, 4669, 4672, 4675, 4678, 4681, 4684, 4687, 4690, 4693, 4696, 4699, 4702, 4705, 4708, 4711, 4714, 4717, 4720, 4723, 4726, 4729, 4732, 4735, 4738, 4741, 4744, 4747, 4750, 4753, 4756, 4759, 4762, 4765, 4768, 4771, 4774, 4777, 4780, 4783, 4786, 4789, 4792, 4795, 4798, 4801, 4804, 4807, 4810, 4813, 4816, 4819, 4822, 4825, 4828, 4831, 4834, 4837, 4840, 4843, 4846, 4849, 4852, 4855, 4858, 4861, 4864, 4867, 4870, 4873, 4876, 4879, 4882, 4885, 4888, 4891, 4894, 4897, 4900, 4903, 4906, 4909, 4912, 4915, 4918, 4921, 4924, 4927, 4930, 4933, 4936, 4939, 4942, 4945, 4948, 4951, 4954, 4957, 4960, 4963, 4966, 4969, 4972, 4975, 4978, 4981, 4984, 4987, 4990, 4993, 4996, 4999, 5002, 5005, 5008, 5011, 5014, 5017, 5020, 5023, 5026, 5029, 5032, 5035, 5038, 5041, 5044, 5047, 5050, 5053, 5056, 5059, 5062, 5065, 5068, 5071, 5074, 5077, 5080, 5083, 5086, 5089, 5092, 5095, 5098, 5101, 5104, 5107, 5110, 5113, 5116, 5119, 5122, 5125, 5128, 5131, 5134, 5137, 5140, 5143, 5146, 5149, 5152, 5155, 5158, 5161, 5164, 5167, 5170, 5173, 5176, 5179, 5182, 5185, 5188, 5191, 5194, 5197, 5200, 5203, 5206, 5209, 5212, 5215, 5218, 5221, 5224, 5227, 5230, 5233, 5236, 5239, 5242, 5245, 5248, 5251, 5254, 5257, 5260, 5263, 5266, 5269, 5272, 5275, 5278, 5281, 5284, 5287, 5290, 5293, 5296, 5299, 5302, 5305, 5308, 5311, 5314, 5317, 5320, 5323, 5326, 5329, 5332, 5335, 5338, 5341, 5344, 5347, 5350, 5353, 5356, 5359, 5362, 5365, 5368, 5371, 5374, 5377, 5380, 5383, 5386, 5389, 5392, 5395, 5398, 5401, 5404, 5407, 5410, 5413, 5416, 5419, 5422, 5425, 5428, 5431, 5434, 5437, 5440, 5443, 5446, 5449, 5452, 5455, 5458, 5461, 5464, 5467, 5470, 5473, 5476, 5479, 5482, 5485, 5488, 5491, 5494, 5497, 5500, 5503, 5506, 5509, 5512, 5515, 5518, 5521, 5524, 5527, 5530, 5533, 5536, 5539, 5542, 5545, 5548, 5551, 5554, 5557, 5560, 5563, 5566, 5569, 5572, 5575, 5578, 5581, 5584, 5587, 5590, 5593
ERROR    | 2022-05-22 20:02:03,395 | You cannot estimate a Maximum Likelihood (ML) starting tree (the default behaviour) when you have columns missing from your data block definitions, because the method we use to estimate the ML tree requires all sites in the alignment to be assigned to a data block. We recommend that you either remove the sites you don't want from your alignment or (if possible) include the missing sites in appropriate data blocks. Failing that, you can use the --no-ml-tree command line option. In this case, a NJ (PhyML) or MP(RaxML) starting tree will be estimated for your analysis.
ERROR    | 2022-05-22 20:02:03,397 | Failed to run. See previous errors.

[Rob Lanfear]

Hi There,

The error message outlines your two options here. Have you tried them?

Rob

[Abaranjitha Muniyasamy]

Thank you for your message. 

Yes, I tried them and got this error.

Exception in thread Thread-120:
Traceback (most recent call last):
  File "/home/amuniyas/.conda/envs/partitionFinder/lib/python2.7/threading.py", line 801, in __bootstrap_inner
    self.run()
  File "/scrfs/storage/amuniyas/home/Fish_Genome_Project/Phylogenetics/Partition_Finder/partitionfinder-2.1.1/partfinder/threadpool.py", line 115, in run
    cmd, args = self.pool.next_task()
  File "/scrfs/storage/amuniyas/home/Fish_Genome_Project/Phylogenetics/Partition_Finder/partitionfinder-2.1.1/partfinder/threadpool.py", line 81, in next_task
    task = self.tasks[self.curtask]
IndexError: list index out of range

[Rob Lanfear]

Can you post the commandline you used?

A couple of things to try here: 

1. Make sure you're starting a fresh analysis

2. If that doesn't work, try running it (at least at the start) on a single thread (the error is with thread handling, which is a fairly rare thing to see happen)

Rob

[Abaranjitha Muniyasamy]

#!/bin/bash

#SBATCH --job-name=Partition_Finder
#SBATCH --partition tres72
#SBATCH --output=cott_aic_partitionFinder.%j.out
#SBATCH --error=cott_aic_partitionFinder.%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=amun...@uark.edu
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
#SBATCH --time=8:00:00



###Load necessary modules
module load python/anaconda-3.8
source /share/apps/bin/conda-3.8.sh
source activate partitionFinder

###Command
python  /home/amuniyas/Fish_Genome_Project/Phylogenetics/Partition_Finder/partitionfinder-2.1.1/PartitionFinder.py  /home/amuniyas/Fish_Genome_Project/Phylogenetics/Partition_Finder/aic_cott

This is the command used Dr Rob. 

[Abaranjitha Muniyasamy]

I am running on single thread and it is still running for more than 4hrs

On Sunday, 22 May 2022 at 21:17:19 UTC-5 rob.l...@gmail.com wrote: