Closed kkmills closed 3 years ago
brantfaircloth
commented
3 years ago Have you checked to see if there is a problem with that specific locus (or moved it to another directory, then tried again on original data minus that file)? Alternatively, can you get raxml to generate a gene tree from that alignment manually?
kkmills
commented
3 years ago So I made a duplicate directory and deleted uce-2012.phylip file, and I noticed there was also a uce-2012.phylip.reduced file in there. There are about 20 loci (out of 1700) that had a .reduced file in the directory. I'm not sure what those are or if it is related to this error. I generated those using the phyluce_align_convert_one_align_to_another command.
But I deleted both the .phylip and .phylip.reduced for uce-2012, and this time it got stuck on uce-2010, which is weird because it seemed to do uce-2010 fine the first time. So I deleted this locus also (it had a .reduced version too), and now it doesn't seem to be processing any loci before giving the error:
phyluce_genetrees_run_raxml_genetrees --input test-phylip/ --output test-output --outgroup cynomyszzz --cores 8 --threads 1
2021-01-15 15:19:11,230 - phyluce_genetrees_run_raxml_genetrees - INFO - ========= Starting phyluce_genetrees_run_raxml_genetrees ========
2021-01-15 15:19:11,231 - phyluce_genetrees_run_raxml_genetrees - INFO - Version: git fatal: not a git repository: '/home/kendall/miniconda3/envs/phyluce/lib/python2.7/site-packages/.git'
2021-01-15 15:19:11,231 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --cores: 8
2021-01-15 15:19:11,232 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --input: /home/kendall/marmot-uces/10_astral/1_gene-trees/test-phylip
2021-01-15 15:19:11,232 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --log_path: None
2021-01-15 15:19:11,232 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --outgroup: cynomyszzz
2021-01-15 15:19:11,233 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --output: /home/kendall/marmot-uces/10_astral/1_gene-trees/test-output
2021-01-15 15:19:11,234 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --quiet: False
2021-01-15 15:19:11,234 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --threads: 1
2021-01-15 15:19:11,234 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --tree_searches: 100
2021-01-15 15:19:11,234 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --verbosity: INFO
The total number of cores in use is 8. This will run
8 concurrent jobs of 1 thread(s). Is this correct [Y/n]? Y
2021-01-15 15:19:13,718 - phyluce_genetrees_run_raxml_genetrees - INFO - 1698 alignments read
Traceback (most recent call last):
File "/home/kendall/miniconda3/envs/phyluce/bin/phyluce_genetrees_run_raxml_genetrees", line 186, in
brantfaircloth
commented
3 years ago the reduced file is what you get when raxml removes unnecessary columns of data. the log files for each locus output by raxml should tell you what is going on. alternatively, you can run a single locus that didn't work manually and check the log produced from that.
Hi Brant,
I am trying to run phyluce_genetrees_run_raxml_genetrees so that I can generate gene trees for ASTRAL, but it is giving an error after it does uce-2012 each time
phyluce_genetrees_run_raxml_genetrees --input batch3-strict-phylip-90p/ --output batch3-90p/ --outgroup cynomyszzz --cores 8 --threads 1 [WARNING] Output directory exists, REMOVE [Y/n]? Y 2021-01-14 16:41:52,114 - phyluce_genetrees_run_raxml_genetrees - INFO - ========= Starting phyluce_genetrees_run_raxml_genetrees ======== 2021-01-14 16:41:52,115 - phyluce_genetrees_run_raxml_genetrees - INFO - Version: git fatal: not a git repository: '/home/kendall/miniconda3/envs/phyluce/lib/python2.7/site-packages/.git' 2021-01-14 16:41:52,117 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --cores: 8 2021-01-14 16:41:52,117 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --input: /home/kendall/marmot-uces/10_astral/1_gene-trees/batch3-strict-phylip-90p 2021-01-14 16:41:52,118 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --log_path: None 2021-01-14 16:41:52,118 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --outgroup: cynomyszzz 2021-01-14 16:41:52,118 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --output: /home/kendall/marmot-uces/10_astral/1_gene-trees/batch3-90p 2021-01-14 16:41:52,119 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --quiet: False 2021-01-14 16:41:52,119 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --threads: 1 2021-01-14 16:41:52,119 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --tree_searches: 100 2021-01-14 16:41:52,119 - phyluce_genetrees_run_raxml_genetrees - INFO - Argument --verbosity: INFO The total number of cores in use is 8. This will run 8 concurrent jobs of 1 thread(s). Is this correct [Y/n]? Y 2021-01-14 16:41:56,728 - phyluce_genetrees_run_raxml_genetrees - INFO - 1700 alignments read name=uce-2209,seconds=115.526082,sites=104 name=uce-2010,seconds=120.841495,sites=109 name=uce-1867,seconds=132.624486,sites=119 name=uce-134,seconds=139.268848,sites=88 name=uce-1512,seconds=157.943661,sites=115 name=uce-1181,seconds=165.439187,sites=112 name=uce-1003,seconds=173.363159,sites=114 name=uce-172,seconds=186.176460,sites=113 name=uce-1868,seconds=151.644705,sites=100 name=uce-2012,seconds=174.120491,sites=126 Traceback (most recent call last): File "/home/kendall/miniconda3/envs/phyluce/bin/phyluce_genetrees_run_raxml_genetrees", line 186, in
main()
File "/home/kendall/miniconda3/envs/phyluce/bin/phyluce_genetrees_run_raxml_genetrees", line 174, in main
trees = pool.map(run_raxml, work)
File "/home/kendall/miniconda3/envs/phyluce/lib/python2.7/multiprocessing/pool.py", line 253, in map
return self.map_async(func, iterable, chunksize).get()
File "/home/kendall/miniconda3/envs/phyluce/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
AttributeError: 'NoneType' object has no attribute 'groups'