weijiasu / tir-learner-rice Goto Github PK

## pre-set parameters
version="2.5"
path="/Users/ohon_ad/Documents/Project_LTR/EDTA/bin/TIR-Learner2.5" #program path
dir=$(pwd) #current work directory
rawFile="/Users/ohon_ad/Documents/Project_LTR/EDTA/bin/TIR-Learner2.5/GCDROM.fna" #the genome file with relative path
grfp="/Users/ohon_ad/Documents/Tools/GenericRepeatFinder-master/bin"
#grfp="$path/../GenericRepeatFinder/bin/"
#grfp="~/las/bin/GenericRepeatFinder/bin/"
species="others" # One of the following "Maize", "Rice" or "others"
len=5000 # Maximum of element length used in GRF
t=4 # CPUs

sh TIR-Learner2.5.sh 
readlink: illegal option -- f
usage: readlink [-n] [file ...]
############################################################ Pre-Processing ###########################################################
usage: pre.py [-h] -g GENOMEFILE -name GENOMENAME
pre.py: error: argument -g/--genomeFile: expected one argument
Jump to Module3
############################################################ Module 3 Begin ###########################################################
Module 3, Step 1: Split Genome and Run GRF program to find Inverted Repeats
usage: RunGRF.py [-h] -g GENOMEFILE -name GENOMENAME -p PATH -t PROCESSER -d
                 CURRENTD -grfp GRFPATH -l TIR_LENGTH
RunGRF.py: error: argument -g/--genomeFile: expected one argument
Module 3, Step 2: Process GRF results
usage: ProcessGRFmite.py [-h] -g GENOMEFILE -name GENOMENAME -p PATH -t
                         PROCESSER -d CURRENTD
ProcessGRFmite.py: error: argument -g/--genomeFile: expected one argument
cp: TIR-Learner/*-p: No such file or directory
Module 3, Step 3: Get dataset
usage: getDataset.py [-h] -name GENOMENAME -p PATH -t PROCESSER -d CURRENTD -g
                     GENOMEFILE
getDataset.py: error: argument -g/--genomeFile: expected one argument
Module 3, Step 4: Check TIR/TSD
cat: *-+-DTA.fa: No such file or directory
cat: *-+-DTC.fa: No such file or directory
cat: *-+-DTH.fa: No such file or directory
cat: *-+-DTM.fa: No such file or directory
cat: *-+-DTT.fa: No such file or directory
cat: *-+-NonTIR.fa: No such file or directory
Module 3, Step 5: Write to Gff
cat: *-+-*-+-*.gff3: No such file or directory
rm: *-+-*-+-*.gff3: No such file or directory
############################################################ Module 3 Finished ########################################################
Get Final GFF
############################################################ Process and Combining three gff files ##################################
Traceback (most recent call last):
  File "/Users/ohon_ad/Documents/Project_LTR/EDTA/bin/TIR-Learner2.5/Module3_New/CombineAll.py", line 75, in <module>
    f_m3=removeDupinSingle("%s.gff3"%(genome_Name+spliter+"Module3"))
  File "/Users/ohon_ad/Documents/Project_LTR/EDTA/bin/TIR-Learner2.5/Module3_New/CombineAll.py", line 57, in removeDupinSingle
    f=pd.read_csv(file,header=None,sep="\t") #shujun
  File "/Users/ohon_ad/anaconda3/envs/TIR-Learner/lib/python3.6/site-packages/pandas/io/parsers.py", line 676, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/Users/ohon_ad/anaconda3/envs/TIR-Learner/lib/python3.6/site-packages/pandas/io/parsers.py", line 448, in _read
    parser = TextFileReader(fp_or_buf, **kwds)
  File "/Users/ohon_ad/anaconda3/envs/TIR-Learner/lib/python3.6/site-packages/pandas/io/parsers.py", line 880, in __init__
    self._make_engine(self.engine)
  File "/Users/ohon_ad/anaconda3/envs/TIR-Learner/lib/python3.6/site-packages/pandas/io/parsers.py", line 1114, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/Users/ohon_ad/anaconda3/envs/TIR-Learner/lib/python3.6/site-packages/pandas/io/parsers.py", line 1891, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 532, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file
Get fasta file
usage: GetAllSeq.py [-h] -g GENOMEFILE -name GENOMENAME -p PATH -t PROCESSER
                    -d CURRENTD
GetAllSeq.py: error: argument -g/--genomeFile: expected one argument
mv: rename TIR-Learner/*FinalAnn*.gff3 to TIR-Learner-Result/*FinalAnn*.gff3: No such file or directory
mv: rename TIR-Learner/*FinalAnn*.fa to TIR-Learner-Result/*FinalAnn*.fa: No such file or directory