Runmode = -2 in Biopython PAML impossible ?
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6 months ago
Chvatil ▴ 60

The question is in the title, I want to calculate dN/dS between two sequences using PAML implemented in biopython but I get this error message :

cml = codeml.Codeml()
cml.alignment = "/beegfs/data/Species_phylogeny/Busco_DNA_seqs_pairs/"+new_pair_name+".fa"
cml.out_file = "/beegfs/data/Species_phylogeny/Codeml_results/results_"+new_pair_name+".txt"
cml.working_dir = "/beegfs/data/Species_phylogeny/Codeml_results/"


#Changes settings
cml.set_options(kappa=1)
cml.set_options(noisy=9)
cml.set_options(CodonFreq=2)
cml.set_options(model=0)
cml.set_options(icode=0)
cml.set_options(kappa=1)
cml.set_options(fix_omega=0)
cml.set_options(omega=0.5)
cml.set_options(NSsites=[0, 1, 2])
cml.set_options(seqtype=1)
cml.set_options(runmode=-2)
cml.print_options()

cml.run(command="/beegfs/data/TOOLS/paml4.9i/bin/codeml",verbose=True)

I get :

  7         runmode | runmode               -2.00
  4         seqtype | seqtype                1.00
 13       CodonFreq | CodonFreq              2.00
 16           model | model                  0.00
 20         NSsites | NSsites                0.00
 22           icode | icode                  0.00
 25           kappa | kappa                  1.00
 26       fix_omega | fix_omega              0.00
 27           omega | omega                  0.50
gaps are removed for pairwise comparison.
CODONML in paml version 4.9i, September 2018

----------------------------------------------
Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT
      TTC |       TCC |       TAC |       TGC
Leu L TTA |       TCA | *** * TAA | *** * TGA
      TTG |       TCG |       TAG | Trp W TGG
----------------------------------------------
Leu L CTT | Pro P CCT | His H CAT | Arg R CGT
      CTC |       CCC |       CAC |       CGC
      CTA |       CCA | Gln Q CAA |       CGA
      CTG |       CCG |       CAG |       CGG
----------------------------------------------
Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT
      ATC |       ACC |       AAC |       AGC
      ATA |       ACA | Lys K AAA | Arg R AGA
Met M ATG |       ACG |       AAG |       AGG
----------------------------------------------
Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT
      GTC |       GCC |       GAC |       GGC
      GTA |       GCA | Glu E GAA |       GGA
      GTG |       GCG |       GAG |       GGG
----------------------------------------------
Nice code, uuh?

Error: runmode?.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/beegfs/data/soft/python_modules/Bio/Phylo/PAML/codeml.py", line 182, in run
    Paml.run(self, ctl_file, verbose, command)
  File "/beegfs/data/soft/python_modules/Bio/Phylo/PAML/_paml.py", line 127, in run
    % (command, result_code))
Bio.Phylo.PAML._paml.PamlError: /beegfs/data/TOOLS/paml4.9i/bin/codeml has failed (return code 255). Run with verbose = True to view error message

and they also ask a tree, but since I'm in pairwise analysis, I do not need a tree.

paml codeml biopython python3 • 272 views
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