Dear All

I am trying to use simple for loop in shell script to execute bacth process of codeml to calculate dn/ds values for 1500 Orthologues but I am getting this error.

    #!/bin/bash

    for file in  *.aln
      do

    `echo $file | sed 's/\.aln//'`

     python codemlScript.py /home/tulasi/Desktop/Tools/Tools/AutoPAML/Alignments/\.aln /home/tulasi/Desktop/Tools/Tools/AutoPAML/Trees/\.tree /home/tulasi/Desktop/Tools/Tools/AutoPAML/Out/\.out

    done

But I am getting this out put with error

    Saureus1202.aln
    Saureus1202.aln
    Saure_omega.out

    25           kappa | kappa                  1.60
    16           model | model                  0.00
    CODONML in paml version 4.8, March 2014

    ----------------------------------------------
    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?


    Ambiguity character definition table:

    T (1): T 
    C (1): C 
    A (1): A 
    G (1): G 
    U (1): T 
    Y (2): T C 
    R (2): A G 
    M (2): C A 
    K (2): T G 
    S (2): C G 
    W (2): T A 
    H (3): T C A 
    B (3): T C G 
    V (3): C A G 
    D (3): T A G 
    - (4): T C A G 
    N (4): T C A G 
    ? (4): T C A G 

    processing fasta file
    reading seq# 1 A27919                                                1359 sites
    reading seq# 2 A15262                                                1359 sites
    reading seq# 3 A23133                                                1359 sites
    reading seq# 4 A10245                                                1359 sites
    reading seq# 5 A2708                                                 1359 sites
     reading seq# 6 A12710                                                1359 sites
     reading seq# 7 A5063                                                 1359 sites
     reading seq# 8 A1                                                    1359 sites
     reading seq# 9 A7706                                                 1359 sites
     reading seq#10 A20825                                                1359 sites
      reading seq#11 A17684                                                1359 sites
      reading seq#12 A25250                                                1359 sites
      ns = 12  	ls = 1359
      Reading sequences, sequential format..
      Reading seq #12: A25250     
      Sequences read..
      Counting site patterns..  0:00
          71 patterns at      453 /      453 sites (100.0%),  0:00
      Counting codons..
      NG distances for seqs.:
      1
      2   1:Sites   298.7 + 1060.3 = 1359.0	Diffs    11.0 +    1.0 =   12.0   2
      3   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
      3   2:Sites   298.7 + 1060.3 = 1359.0	Diffs     4.0 +    0.0 =    4.0   3
      4   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
      4   2:Sites   298.7 + 1060.3 = 1359.0	Diffs     4.0 +    0.0 =    4.0
      4   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     0.0 +    0.0 =    0.0   4
      5   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
      5   2:Sites   298.7 + 1060.3 = 1359.0	Diffs     4.0 +    0.0 =    4.0
      5   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     0.0 +    0.0 =    0.0
      5   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     0.0 +    0.0 =    0.0   5
      6   1:Sites   298.8 + 1060.2 = 1359.0	Diffs     0.0 +    0.0 =    0.0
      6   2:Sites   298.7 + 1060.3 = 1359.0	Diffs    11.0 +    1.0 =   12.0
      6   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
      6   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
      6   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0   6
      7   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     4.0 +    1.0 =    5.0
      7   2:Sites   298.7 + 1060.3 = 1359.0	Diffs    11.0 +    0.0 =   11.0
      7   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    0.0 =    7.0
      7   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    0.0 =    7.0
      7   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    0.0 =    7.0
      7   6:Sites   298.7 + 1060.3 = 1359.0	Diffs     4.0 +    1.0 =    5.0   7
      8   1:Sites   298.7 + 1060.3 = 1359.0	Diffs    10.0 +    1.0 =   11.0
      8   2:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
      8   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
      8   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
      8   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
      8   6:Sites   298.7 + 1060.3 = 1359.0	Diffs    10.0 +    1.0 =   11.0
      8   7:Sites   298.6 + 1060.4 = 1359.0	Diffs    10.0 +    0.0 =   10.0   8
      9   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    1.0 =    4.0
      9   2:Sites   298.7 + 1060.3 = 1359.0	Diffs    10.0 +    0.0 =   10.0
      9   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    0.0 =    6.0
      9   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    0.0 =    6.0
      9   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    0.0 =    6.0
      9   6:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    1.0 =    4.0
     9   7:Sites   298.6 + 1060.4 = 1359.0	Diffs     1.0 +    0.0 =    1.0
     9   8:Sites   298.6 + 1060.4 = 1359.0	Diffs     9.0 +    0.0 =    9.0   9
    10   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    1.0 =    7.0
    10   2:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    0.0 =    7.0
    10   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
    10   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
    10   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    0.0 =    3.0
    10   6:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    1.0 =    7.0
    10   7:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    0.0 =    6.0
    10   8:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    0.0 =    6.0
    10   9:Sites   298.7 + 1060.3 = 1359.0	Diffs     5.0 +    0.0 =    5.0  10
    11   1:Sites   298.7 + 1060.3 = 1359.0	Diffs     8.0 +    2.0 =   10.0
    11   2:Sites   298.7 + 1060.3 = 1359.0	Diffs    11.0 +    1.0 =   12.0
    11   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
    11   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
    11   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
    11   6:Sites   298.7 + 1060.3 = 1359.0	Diffs     8.0 +    2.0 =   10.0
    11   7:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    1.0 =    7.0
    11   8:Sites   298.7 + 1060.3 = 1359.0	Diffs    10.0 +    1.0 =   11.0
    11   9:Sites   298.7 + 1060.3 = 1359.0	Diffs     5.0 +    1.0 =    6.0
    11  10:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    1.0 =    7.0  11
    12   1:Sites   298.8 + 1060.2 = 1359.0	Diffs     0.0 +    0.0 =    0.0
    12   2:Sites   298.7 + 1060.3 = 1359.0	Diffs    11.0 +    1.0 =   12.0
    12   3:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
    12   4:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
    12   5:Sites   298.7 + 1060.3 = 1359.0	Diffs     7.0 +    1.0 =    8.0
     12   6:Sites   298.8 + 1060.2 = 1359.0	Diffs     0.0 +    0.0 =    0.0
    12   7:Sites   298.7 + 1060.3 = 1359.0	Diffs     4.0 +    1.0 =    5.0
    12   8:Sites   298.7 + 1060.3 = 1359.0	Diffs    10.0 +    1.0 =   11.0
     12   9:Sites   298.7 + 1060.3 = 1359.0	Diffs     3.0 +    1.0 =    4.0
    12  10:Sites   298.7 + 1060.3 = 1359.0	Diffs     6.0 +    1.0 =    7.0
     12  11:Sites   298.7 + 1060.3 = 1359.0	Diffs     8.0 +    2.0 =   10.0  12

      528 bytes for distance
    69296 bytes for conP
        0 bytes for fhK
     5000000 bytes for space
     . (Continuation of codeml output)
      .
       .   
     w =  0.02373 dN =  0.00000 dS =  0.00001 d4 =  0.00000 (189.6 four-fold sites)
             dN*=  0.00000 dS*=  0.00001 S* = 315.11 N* =1043.89
     end of tree file.

    Time used:  0:10
    Saureus1203.aln
    Saureus1203.aln
     Saure_omega.out
     Traceback (most recent call last):
       File "codemlScript.py", line 45, in <module>
       results = cml.run(verbose=True)
        File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/codeml.py", line 185, in run
    raise IOError("The specified tree file does not exist.")
      IOError: The specified tree file does not exist.

This is the pyhthon script I got from github 

     #!/usr/bin/python
     
      ###################################################################################################################
    #This script was written by Nathan Whelan.

    # THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS  
    # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF  MERCHANTABILITY,
    # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
    # THE CONTRIBUTORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
    # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF
    # OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE
    # SOFTWARE.
    ##########################################################################################################################

    ##This script utilizes codeml in PAML by Ziheng Yang. If you use this script please also cite PAML.

    ##BIOPYTHON IS REQUIRED FOR THIS SCRIPT!

    ##This script can be used to automate running the codeml PAML package(e.g. if you have hundreds of genes you want to fit to a model).
    #A codeml ctl file should be in your working directory with the parameters you wish to use.

    from __future__ import division
    from Bio.Phylo.PAML import codeml ##Biopython PAML
    import sys

    #This program takes three inputs: the alignment in phylip format, a treefile in Newick format, and outputfile name
    #It returns a nested dictionary with various results depending on analysis
    if len(sys.argv) != 4:
    print "Error.  There should be three inputs. An alignment in pyhlip format, a tree file, and the name for the     output file"
    quit()

    cml = codeml.Codeml()
    cml.read_ctl_file("codeml.ctl") ##CTL File. See PAML manual for format.
    cml.alignment = sys.argv[1]
    cml.tree = sys.argv[2]
    cml.out_file = sys.argv[3]

    name=sys.argv[1]
    print name
    name=sys.argv[1]
    print name
    name2=name[0:5]+"omega.out"
    print name2
    results1 = cml.run(verbose=True)

I would like to know where I am doing mistake..

I guess now we need small modification in python script but i don't know where.
Please try to solve 

Thank you
try

    ls *.phy.aln |  sed 's/_DNA.phy.aln//' | while read NAME; do python codemlScript.py "${NAME}_DNA.phy.aln" "${NAME}_dropped.tre" "${NAME}_PAML_NeutralMethod1.out" ; done

