Error after ete3 evol

[Jessica Maccaro]

Hi there, 

I ran the following two loops for different analyses and got errors associated with both. Many of the orthologs worked just fine but some had the errors below. Can you please tell me what these errors could mean? 

#Loop for first models I ran 

for ALNUC in $(ls ALNUCsimplenames_fa/*.fa)
do
NAMEBASE=$(basename -s .fa $ALNUC)
NT_FILENAME="${NAMEBASE}.fa"
echo "Processing $NAMEBASE"
ete3 evol -t ALNUCsimplenames_fa/SpeciesTree_simple_names.txt --alg ALNUCsimplenames_fa/$NT_FILENAME --models bsA bsA1 --mark Aagg=AAP Aagg,,AAP Aagg AAP -o site_model_results/$NAMEBASE
done >> sum_output_site_model.out 2>&1

Error: 

Processing OG0001698

Using: /Users/melittology_lab/anaconda3/envs/py27/bin/ete3_apps/bin/Slr
Using: /Users/melittology_lab/anaconda3/envs/py27/bin/ete3_apps/bin/codeml

Running CodeML/Slr (16 CPUs)
mkdir: 4_genome_brst_model_results/OG0001698/bsA.7-1~3f30c26297b6e896a8de84ed1d32bb60: Input/output error
  - processing model bsA (bsA~4118e07d76f068bdf222e4de40145b2b)
       marking branches 3, 1

          (Aatr,(Aace,(Aagg #1,AAP #1)));

       marking branches 7

          (Aatr,(Aace,(Aagg,AAP) #1));

       marking branches 3

          (Aatr,(Aace,(Aagg #1,AAP)));

       marking branches 1

          (Aatr,(Aace,(Aagg,AAP #1)));

  - processing model bsA1 (bsA1~0d98b332b5465ebdad5b4068ab8c1592)
       marking branches 3, 1

          (Aatr,(Aace,(Aagg #1,AAP #1)));

       marking branches 7

          (Aatr,(Aace,(Aagg,AAP) #1));

       marking branches 3

          (Aatr,(Aace,(Aagg #1,AAP)));

       marking branches 1

          (Aatr,(Aace,(Aagg,AAP #1)));

Traceback (most recent call last):
  File "/Users/melittology_lab/anaconda3/envs/py27/bin/ete3", line 10, in <module>
    sys.exit(main())
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete.py", line 95, in main
    _main(sys.argv)
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete.py", line 268, in _main
    args.func(args)
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete_evol.py", line 900, in run
    models.update(run_all_models(tree, nodes, marks, args, **params))
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete_evol.py", line 590, in run_all_models
    path, model = result.get()
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 572, in get
    raise self._value
IOError: [Errno 2] No such file or directory: '4_genome_brst_model_results/OG0001698/bsA.7-1~3f30c26297b6e896a8de84ed1d32bb60/algn'

#Second model ran (this one had way more orthologs with errors) 

for ALNUC in $(ls FinalNucs_0.9/*.fa)

do
NAMEBASE=$(basename -s .fa $ALNUC)
NT_FILENAME="${NAMEBASE}.fa"
echo "Processing $NAMEBASE"
ete3 evol -t FinalNucs_0.9/SpeciesTree_simple_names.txt --alg FinalNuc_0.9/$NT_FILENAME --models bsA bsA1 --mark Aace=Apol=Aatr --cpu 16 -o branch_site_model_results_commsGOOD/$NAMEBASE
done >> sum_output_commsGOOD.out 2>&1

error: 

Processing OG0001692

Using: /Users/melittology_lab/anaconda3/envs/py27/bin/ete3_apps/bin/Slr
Using: /Users/melittology_lab/anaconda3/envs/py27/bin/ete3_apps/bin/codeml

Running CodeML/Slr (16 CPUs)
mkdir: 4Gencom_brst_model_results/OG0001692/bsA1.2_4-1_1~d74e937b8f5bc71e46897741f5ff4dee: Input/output error
  - processing model bsA (bsA~4118e07d76f068bdf222e4de40145b2b)
       marking branches 2, 4

          (Aatr #1,(Aace #1,(Aagg,AAP)));

  - processing model bsA1 (bsA1~0d98b332b5465ebdad5b4068ab8c1592)
       marking branches 2, 4

          (Aatr #1,(Aace #1,(Aagg,AAP)));

Traceback (most recent call last):
  File "/Users/melittology_lab/anaconda3/envs/py27/bin/ete3", line 10, in <module>
    sys.exit(main())
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete.py", line 95, in main
    _main(sys.argv)
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete.py", line 268, in _main
    args.func(args)
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete_evol.py", line 900, in run
    models.update(run_all_models(tree, nodes, marks, args, **params))
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/site-packages/ete3/tools/ete_evol.py", line 590, in run_all_models
    path, model = result.get()
  File "/Users/melittology_lab/anaconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 572, in get
    raise self._value
IOError: [Errno 2] No such file or directory: '4Gencom_brst_model_results/OG0001692/bsA1.2_4-1_1~d74e937b8f5bc71e46897741f5ff4dee/algn'

These models both used the same fasta files (which were all the single copy orthologs between 4 species). I attached the two files that had errors in the above examples. There are several with the same error so I just wanted to see what it meant. The alignments aren't very good for these but there were several alignments that were not great that did work still, so I'm not sure it's that.  

Let me know what you think and thanks so much. 

Best, 

Jess