############################################################ Pre-Processing ###########################################################
2 sequences in genome file TIR-Learner
############################################################ Module 1 Begin ###########################################################
Module 1, Step 1: Blast Genome against Reference Library


Building a new DB, current time: 06/24/2019 09:19:19
New DB name:   genome.fasta-+-db
New DB title:  genome.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 2 sequences in 0.040338 seconds.
FASTA-Reader: Ignoring invalid residues at position(s): On line 250: 1224-1597, 1622-1750
FASTA-Reader: Ignoring invalid residues at position(s): On line 252: 520-746
FASTA-Reader: Ignoring invalid residues at position(s): On line 254: 1936-2299
FASTA-Reader: Ignoring invalid residues at position(s): On line 380: 5993-6353
FASTA-Reader: Ignoring invalid residues at position(s): On line 386: 238-242, 1481-1485, 2106-2110, 3127-3131
FASTA-Reader: Ignoring invalid residues at position(s): On line 472: 268-272
FASTA-Reader: Ignoring invalid residues at position(s): On line 534: 225-229
FASTA-Reader: Ignoring invalid residues at position(s): On line 566: 11-15
No Blast Result, Jump to Module3
############################################################ Module 3 Begin ###########################################################
Module 3, Step 1: Split Genome and  Run GRF program to find Inverted Repeats
start: Mon Jun 24 09:19:33 2019

calculate cumulative scores in chromosome scaffold_2: Mon Jun 24 09:19:33 2019

find candidates in chromosome scaffold_2: Mon Jun 24 09:19:33 2019

print: Mon Jun 24 09:23:59 2019

end: Mon Jun 24 09:23:59 2019

start: Mon Jun 24 09:23:59 2019

calculate cumulative scores in chromosome scaffold_1: Mon Jun 24 09:23:59 2019

find candidates in chromosome scaffold_1: Mon Jun 24 09:23:59 2019

print: Mon Jun 24 09:29:28 2019

end: Mon Jun 24 09:29:29 2019

Module 2, Step 2: Process GRF results
rm: cannot remove 'TIR-Learner-+-scaffold_1.fa': No such file or directory
rm: cannot remove 'TIR-Learner-+-scaffold_2.fa': No such file or directory
Module 3, Step 3: Get dataset
Module 3, Step 4: ML prediction
Module 3, Step 5: Check TIR/TSD
rm: cannot remove '*_DTA.fa': No such file or directory
rm: cannot remove '*_DTC.fa': No such file or directory
rm: cannot remove '*_DTH.fa': No such file or directory
rm: cannot remove '*_DTM.fa': No such file or directory
rm: cannot remove '*_DTT.fa': No such file or directory
Module 3, Step 6: Write to Gff
Module 3, Step 7: Remove Low complexity
############################################################ Module 3 Finished ###########################################################
Get Final GFF
cp: cannot stat 'Module3/TIR-Learner/TIR-Learner-+-Module3.gff3': No such file or directory
cp: cannot stat 'Module3/TIR-Learner/TIR-Learner-+-Module3-+-Low': No such file or directory
############################################################################## Removing Entries with Homology in Flanking Sequences ##################################
Traceback (most recent call last):
  File "~/bin/EDTA-TIR-Learner1.13/bin/TIR-Learner1.13/Module3_New/CombineAll.py", line 91, in <module>
    remove = FlankingBlast("%sLow"%(genome_Name+spliter+dataset+spliter))
  File "~/bin/EDTA-TIR-Learner1.13/bin/TIR-Learner1.13/Module3_New/CombineAll.py", line 37, in FlankingBlast
    f=open(file,"r+")
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-Module3-+-Low'
mv: cannot stat '*.gff3': No such file or directory
rm: cannot remove '*Low': No such file or directory
Get fasta file
Traceback (most recent call last):
  File "~/bin/EDTA-TIR-Learner1.13/bin/TIR-Learner1.13/Module3_New/GetAllSeq.py", line 60, in <module>
    file=open(f,"r+")
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner_FinalAnn.gff3'
mv: cannot stat 'TIR-Learner/*FinalAnn.gff3': No such file or directory
mv: cannot stat 'TIR-Learner/*FinalAnn.fa': No such file or directory
############################################################ TIR-Learner is finished! ###########################################################