Can't find label error about edta HOT 4 CLOSED

I have the same issue than above.

This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

from edta.

Dear @QiushiLi @ofedrigo,

Thank you for using EDTA. I just finished a major upgrade for the program, please reinstall it and help to test with your genomes. Please ignore the FASTA-Reader error (e.g. FASTA-Reader: Ignoring invalid residues at position(s): On line 252: 520-746) and cp rm errors for now. They are harmless to the result.

Please kindly let me know if you encounter any other errors. Thank you!

Best,
Shujun

from edta.

Dear Shujun,

My pleasure to run the test. Please see the this full screen output with some fatal errors. Seems like caused by some Glibc absence?

Thanks,
Qiushi

CMD:
perl /data/home/qiushi_volumn1/programs/EDTA/EDTA.pl -genome path/to/genome.fa -threads 36

########################################################

Extensive de-novo TE Annotator (EDTA) v1.2

Shujun Ou ([email protected])

########################################################

Tue Jun 18 03:19:53 MDT 2019 Dependency checking:
All passed!
Tue Jun 18 03:19:57 MDT 2019 Obtain raw TE libraries using various structure-based programs:
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 534: 225-229
FASTA-Reader: Ignoring invalid residues at position(s): On line 566: 11-15
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
Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module1/Fullcov.py", line 52, in
ProcessHomology(genome_Name)
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module1/Fullcov.py", line 41, in ProcessHomology
f = pd.read_csv(blast, header=None, sep="\t")
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/pandas/io/parsers.py", line 702, in parser_f
return _read(filepath_or_buffer, kwds)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/pandas/io/parsers.py", line 429, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/pandas/io/parsers.py", line 895, in init
self._make_engine(self.engine)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/pandas/io/parsers.py", line 1122, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/pandas/io/parsers.py", line 1853, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 545, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
cat: *DTA-+-select.fa: No such file or directory
cat: *DTC-+-select.fa: No such file or directory
cat: DTH-+-select.fa: No such file or directory
cat: DTM-+-select.fa: No such file or directory
cat: DTT-+-select.fa: No such file or directory
cat: -+--+-.gff3: No such file or directory
Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module1/Lowcomp_M1.py", line 84, in
records = list(SeqIO.parse(genome_Name+spliter+"F200.fa", "fasta"))
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 636, in parse
with as_handle(handle, mode) as fp:
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/contextlib.py", line 81, in enter
return next(self.gen)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/File.py", line 113, in as_handle
with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-F200.fa'
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.20' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main) /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/../GenericRepeatFinder/bin//grf-main)
cp: cannot stat ‘chrI/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrIII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrIV/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrIX/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrM/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrUn/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrV/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrVI/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrVII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrVIII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrX/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXI/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXIII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXIV/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXIX/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXV/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXVI/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXVII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXVIII/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXX/candidate.fasta’: No such file or directory
cp: cannot stat ‘chrXXI/candidate.fasta’: No such file or directory
cp: cannot stat ‘TIR-Learner/-p’: No such file or directory
cp: cannot stat ‘/_RefLib’: No such file or directory
cat: chrI80.fa: No such file or directory
cat: chrII80.fa: No such file or directory
cat: chrIII80.fa: No such file or directory
cat: chrIV80.fa: No such file or directory
cat: chrIX80.fa: No such file or directory
cat: chrM80.fa: No such file or directory
cat: chrUn80.fa: No such file or directory
cat: chrV80.fa: No such file or directory
cat: chrVI80.fa: No such file or directory
cat: chrVII80.fa: No such file or directory
cat: chrVIII80.fa: No such file or directory
cat: chrX80.fa: No such file or directory
cat: chrXI80.fa: No such file or directory
cat: chrXII80.fa: No such file or directory
cat: chrXIII80.fa: No such file or directory
cat: chrXIV80.fa: No such file or directory
cat: chrXIX80.fa: No such file or directory
cat: chrXV80.fa: No such file or directory
cat: chrXVI80.fa: No such file or directory
cat: chrXVII80.fa: No such file or directory
cat: chrXVIII80.fa: No such file or directory
cat: chrXX80.fa: No such file or directory
cat: chrXXI80.fa: No such file or directory
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module2/GetSeq_M2.py", line 74, in getNonHomo
records_all=list(SeqIO.parse(allSeq,"fasta"))
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 636, in parse
with as_handle(handle, mode) as fp:
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/contextlib.py", line 81, in enter
return next(self.gen)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/File.py", line 113, in as_handle
with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-chrIX-+-GRFmite.fa-+-p'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module2/GetSeq_M2.py", line 101, in
pool.map(getNonHomo,l_list)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/multiprocessing/pool.py", line 266, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-chrIX-+-GRFmite.fa-+-p'
cat: DTA_RefLib-+-80.fa: No such file or directory
rm: cannot remove ‘DTA_RefLib-+-80’: No such file or directory
rm: cannot remove ‘DTA_RefLib-+-80.fa’: No such file or directory
cat: DTC_RefLib-+-80.fa: No such file or directory
rm: cannot remove ‘DTC_RefLib-+-80’: No such file or directory
rm: cannot remove ‘DTC_RefLib-+-80.fa’: No such file or directory
cat: DTH_RefLib-+-80.fa: No such file or directory
rm: cannot remove ‘DTH_RefLib-+-80’: No such file or directory
rm: cannot remove ‘DTH_RefLib-+-80.fa’: No such file or directory
cat: DTM_RefLib-+-80.fa: No such file or directory
rm: cannot remove ‘DTM_RefLib-+-80’: No such file or directory
rm: cannot remove ‘DTM_RefLib-+-80.fa’: No such file or directory
cat: DTT_RefLib-+-80.fa: No such file or directory
rm: cannot remove ‘DTT_RefLib-+-80’: No such file or directory
rm: cannot remove ‘DTT_RefLib-+-80.fa’: No such file or directory
rm: cannot remove ‘./-+-p’: No such file or directory
rm: cannot remove ‘./-+-p’: No such file or directory
rm: cannot remove ‘./-+-homo.fa’: No such file or directory
rm: cannot remove ‘./-+-p’: No such file or directory
rm: cannot remove ‘./-+-homo.fa’: No such file or directory
rm: cannot remove ‘./-+-p’: No such file or directory
rm: cannot remove ‘./-+-homo.fa’: No such file or directory
rm: cannot remove ‘./-+-p’: No such file or directory
rm: cannot remove ‘./-+-homo.fa’: No such file or directory
cat: -+--+-.gff3: No such file or directory
rm: cannot remove ‘-+--+-.gff3’: No such file or directory
rm: cannot remove ‘homo-+-80.fa’: No such file or directory
Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module2/Lowcomp_M2.py", line 85, in
records = list(SeqIO.parse(genome_Name+spliter+"M2F200.fa", "fasta"))
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 636, in parse
with as_handle(handle, mode) as fp:
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/contextlib.py", line 81, in enter
return next(self.gen)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/File.py", line 113, in as_handle
with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-M2F200.fa'
mv: cannot stat ‘../Module2/TIR-Learner/_nonHomo.fa’: No such file or directory
cp: cannot stat ‘TIR-Learner/.csv’: No such file or directory
cp: cannot stat ‘TIR-Learner/nonHomo.fa’: No such file or directory
cat: DTA.fa: No such file or directory
rm: cannot remove ‘_DTA.fa’: No such file or directory
cat: DTC.fa: No such file or directory
rm: cannot remove ‘_DTC.fa’: No such file or directory
cat: DTH.fa: No such file or directory
rm: cannot remove ‘_DTH.fa’: No such file or directory
cat: DTM.fa: No such file or directory
rm: cannot remove ‘_DTM.fa’: No such file or directory
cat: DTT.fa: No such file or directory
rm: cannot remove ‘_DTT.fa’: No such file or directory
rm: cannot remove ‘.csv’: No such file or directory
rm: cannot remove ‘_nonHomo.fa’: No such file or directory
cat: -+--+-.gff3: No such file or directory
rm: cannot remove ‘-+--+-.gff3’: No such file or directory
Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/Module3/Lowcomp_M3.py", line 86, in
records = list(SeqIO.parse(genome_Name+spliter+"M3F200.fa", "fasta"))
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 636, in parse
with as_handle(handle, mode) as fp:
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/contextlib.py", line 81, in enter
return next(self.gen)
File "/data/qiushi/anaconda3/envs/EDTA/lib/python3.6/site-packages/Bio/File.py", line 113, in as_handle
with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-M3F200.fa'
cp: cannot stat ‘Module1/TIR-Learner/TIR-Learner-+-Module1-+-Low’: No such file or directory
cp: cannot stat ‘Module2/TIR-Learner/TIR-Learner-+-Module2-+-Low’: No such file or directory
cp: cannot stat ‘Module3/TIR-Learner/TIR-Learner-+-Module3-+-Low’: No such file or directory
Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/CombineAll.py", line 91, in
remove = FlankingBlast("%sLow"%(genome_Name+spliter+dataset+spliter))
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/CombineAll.py", line 37, in FlankingBlast
f=open(file,"r+")
FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner-+-Module1-+-Low'
rm: cannot remove ‘*Low’: No such file or directory
Traceback (most recent call last):
File "/data/home/qiushi_volumn1/programs/EDTA/bin/TIR-Learner1.12/GetAllSeq.py", line 60, in
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
cp: cannot stat ‘TIR-Learner-Result/TIR-Learner_FinalAnn.fa’: No such file or directory
Error: TIR results not found!

ERROR: Raw TIR results not found in genome.fa.EDTA.raw/genome.fa.TIR.raw.fa at /data/home/qiushi_volumn1/programs/EDTA/EDTA.pl line 137.

from edta.

Hi @QiushiLi @ofedrigo ,

Sorry for the bug. Please refer to #4 for a test version of EDTA. Please let me know if there is any error in this version.

Best,
Shujun

from edta.