<< Program name: bch_pbs_classify_msa_errors.D2.pl (path: bch_pbs_classify_msa_errors.D2.pl) >>

Sequence Type: Nucleotide Sequences.

< Parameters for the Tree Inference >

Executable program: /Users/kezawa3/Bioinformatics/PhyML/Compiled/bin/phyml .
Substitution model: TN93 .
#{Substitution rate categories} = 1 .
{Gamma shape parameter for rate variation across sites} = 0 .
Option for the residue frequency: --resfreq=0.25,0.25,0.25,0.25 .
Transition/Transversion Ratios:
   (For A<->G) 1 ,
   (For T<->C) 1 .

Topology search method: NNI .

< Input/Output files/directories >

Hostname: Ezawa-Kiyoshi-no-Mac-Pro.local .
Current working directory: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation .

Master Perl script: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/Scripts/classify_msa_errors_via_mblks.2val.pl .
Template of the scripts to be submitted via Grid Engine: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/Scripts/pbs_classify_msa_errors.mac.D2.sh .

{Input MSA type} = 15mammals .
{Aligner type}   = PRANK/Best_Match .

Main Input archives: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Erroneous_Regions/PRANK/Best_Match/15mammals/Outputs/class_{ID_class}.tgz ,
          where {ID_class} = 0001 .

Temporary input MSAs (reference):     TEST_Outputs/Test_PRANK/Temporary/class_{ID_class}/refaln.{local_MSA_ID}.aln ,
Temporary input MSAs (reconstructed): TEST_Outputs/Test_PRANK/Temporary/class_{ID_class}/recaln.{local_MSA_ID}.aln ,
Input tree and indel parameters:      TEST_Outputs/Test_PRANK/Temporary/class_{ID_class}/dawg_inp{local_MSA_ID}.txt .

1st Subsidiary Input archives: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Erroneous_Regions/Equiv_Regions/PRANK/Best_Match/15mammals/Outputs/class_{ID_class}.tgz .

List of disagreeing segments:      TEST_Outputs/Test_PRANK/Temporary/class_{ID_class}/equiv_rgs_brief.{local_MSA_ID}.txt .

Output Directories: {outdir} = {top_dir}/lclid_{local_MSA_ID} ,
PBS job Scripts:   {top_dir}/PBS_scripts/pbs_classify_msa_errors.{local_MSA_ID}.sh ,
Log Files for PBS jobs: {top_dir}/Log_PBS/log_pbs_classify_msa_errors.{local_MSA_ID}.txt ,
   where {division}'s are the same as those for the input files ,
   and {top_dir} = TEST_Outputs/Test_PRANK/class_{ID_class} is the top output directory for each class of MSAs.

Directories for the Interim Outputs: {outdir}/Interim .

Start: 2015年 12月28日 月曜日 20時23分53秒 JST

[INFORMATION] Successfully converted the relative path, "TESTs/Test_PRANK/Temporary," of the temporary input/output directory into the absolute path, "/Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TESTs/Test_PRANK/Temporary" ...

<< Class: 0001 >>

#{Input MSAs in the archive} = 5 .

< Input MSA ID: 0000001 >

 The job for the division 0000001 has been done .

 ... Successfully extracted some input sequences, and classified the MSA errors into a number of types ...

< Input MSA ID: 0000002 >

 The job for the division 0000002 has been done .

 ... Successfully extracted some input sequences, and classified the MSA errors into a number of types ...

< Input MSA ID: 0000003 >

 The job for the division 0000003 has been done .

 ... Successfully extracted some input sequences, and classified the MSA errors into a number of types ...

< Input MSA ID: 0000004 >

 The job for the division 0000004 has been done .

 ... Successfully extracted some input sequences, and classified the MSA errors into a number of types ...

< Input MSA ID: 0000005 >

 The job for the division 0000005 has been done .

 ... Successfully extracted some input sequences, and classified the MSA errors into a number of types ...


... Successfully archived the masked MSAs into 'class_0001.tgz' under 'TESTs/Test_PRANK'!!


=== All Processes FINISHED !! ===

#{MSA Classes} = 1 .
#{Input MSAs}  = 5 .
    #{Anomalous} = 0 ,
    #{Failed}    = 0 ,
    #{Succeeded} = 5 .

2015年 12月28日 月曜日 20時24分07秒 JST


real	0m13.494s
user	0m7.317s
sys	0m3.348s
