Can't find label error

[QiushiLi]

Dear Shujun,

Please see this error,

Dependency checking: All passed!
Can't find label ALL at /data/home/qiushi_volumn1/programs/EDTA/EDTA.pl line 118.

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

Many thanks~
Your loyal fans

[ofedrigo]

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

[oushujun]

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

[QiushiLi]

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 (shujun.ou.1@gmail.com)

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

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.

[oushujun]

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