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oushujun
ERROR: No candidate is found in the file(s) you specified.
Hi shujun,
When I'm running the EDTA process, I'm getting an error that I can't fix. I have pasted my log file as below, I hope to get your help.
Best, Xu
########################################################
Extensive de-novo TE Annotator (EDTA) v2.0.1
Shujun Ou ([email protected])
########################################################
2022年 07月 26日 星期二 22:28:33 CST Dependency checking: All passed!
2022年 07月 26日 星期二 22:28:39 CST Obtain raw TE libraries using various structure-based programs: 2022年 07月 26日 星期二 22:28:40 CST EDTA_raw: Check dependencies, prepare working directories.
2022年 07月 26日 星期二 22:28:45 CST Start to find LTR candidates.
2022年 07月 26日 星期二 22:28:45 CST Identify LTR retrotransposon candidates from scratch.
2022年 07月 26日 星期二 22:28:45 CST Existing raw result aa.fa.mod.harvest.scn found! Will use this for further analyses.
2022年 07月 26日 星期二 22:28:45 CST Existing raw result aa.fa.mod.finder.combine.scn found! Will use this for further analyses.
ERROR: No candidate is found in the file(s) you specified.
awk: fatal: cannot open file `aa.fa.mod.pass.list' for reading (没有那个文件或目录) Warning: LOC list - is empty.
perl rename_LTR_skim.pl target_sequence.fa LTR_retriever.defalse
Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3
2022年 07月 26日 星期二 22:29:04 CST Warning: The LTR result file has 0 bp!
2022年 07月 26日 星期二 22:29:04 CST Start to find TIR candidates.
2022年 07月 26日 星期二 22:29:04 CST Identify TIR candidates from scratch.
Species: others
cat: '-+--+-.gff3': 没有那个文件或目录
rm: 无法删除 '-+--+-.gff3': 没有那个文件或目录
Traceback (most recent call last):
File "/120t/caix/src/EDTA/test/EDTA-2.0.1/bin/TIR-Learner2.5/Module3_New/CombineAll.py", line 75, in
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/120t/caix/src/EDTA/test/EDTA-2.0.1/bin/TIR-Learner2.5/Module3/GetAllSeq.py", line 63, in
Error: Error while loading sequenceCan't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: 没有那个文件或目录. Warning: The TIR result file has 0 bp!
2022年 07月 26日 星期二 22:29:26 CST Start to find Helitron candidates.
2022年 07月 26日 星期二 22:29:26 CST Identify Helitron candidates from scratch.
Warning: LOC list aa.fa.mod.HelitronScanner.raw.ext.list is empty. Warning: LOC list aa.fa.mod.HelitronScanner.raw.ext.list is empty.
Error: Error while loading sequence perl make_bed_with_intact.pl EDTA.intact.fa > EDTA.intact.bed
2022年 07月 26日 星期二 22:29:42 CST Warning: The Helitron result file has 0 bp!
2022年 07月 26日 星期二 22:29:42 CST Execution of EDTA_raw.pl is finished!
ERROR: Raw LTR results not found in aa.fa.mod.EDTA.raw/aa.fa.mod.LTR.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check
It says it cannot find any LTR, TIR, and Helitron in your input file.
Shujun
On Tue, Jul 26, 2022 at 10:37 AM Xu Cai @.***> wrote:
Hi shujun,
When I'm running the EDTA process, I'm getting an error that I can't fix. I have pasted my log file as below, I hope to get your help.
Best, Xu
######################################################## Extensive de-novo TE Annotator (EDTA) v2.0.1 Shujun Ou ( @.***)
########################################################
2022年 07月 26日 星期二 22:28:33 CST Dependency checking: All passed!
2022年 07月 26日 星期二 22:28:39 CST Obtain raw TE libraries using various structure-based programs: 2022年 07月 26日 星期二 22:28:40 CST EDTA_raw: Check dependencies, prepare working directories.
2022年 07月 26日 星期二 22:28:45 CST Start to find LTR candidates.
2022年 07月 26日 星期二 22:28:45 CST Identify LTR retrotransposon candidates from scratch.
2022年 07月 26日 星期二 22:28:45 CST Existing raw result aa.fa.mod.harvest.scn found! Will use this for further analyses.
2022年 07月 26日 星期二 22:28:45 CST Existing raw result aa.fa.mod.finder.combine.scn found! Will use this for further analyses.
ERROR: No candidate is found in the file(s) you specified.
awk: fatal: cannot open file `aa.fa.mod.pass.list' for reading (没有那个文件或目录) Warning: LOC list - is empty.
perl rename_LTR_skim.pl target_sequence.fa LTR_retriever.defalse
Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3
2022年 07月 26日 星期二 22:29:04 CST Warning: The LTR result file has 0 bp!
2022年 07月 26日 星期二 22:29:04 CST Start to find TIR candidates.
2022年 07月 26日 星期二 22:29:04 CST Identify TIR candidates from scratch.
Species: others cat: '-+--+- .gff3': 没有那个文件或目录 rm: 无法删除 '-+--+-.gff3': 没有那个文件或目录 Traceback (most recent call last): File "/120t/caix/src/EDTA/test/EDTA-2.0.1/bin/TIR-Learner2.5/Module3_New/CombineAll.py", line 75, in f_m3=removeDupinSingle("%s.gff3"%(genome_Name+spliter+"Module3")) File "/120t/caix/src/EDTA/test/EDTA-2.0.1/bin/TIR-Learner2.5/Module3_New/CombineAll.py", line 57, in removeDupinSingle f=pd.read_csv(file,header=None,sep="\t") #shujun File "/120t/caix/anaconda3/envs/edta/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv return _read(filepath_or_buffer, kwds) File "/120t/caix/anaconda3/envs/edta/lib/python3.6/site-packages/pandas/io/parsers.py", line 454, in _read parser = TextFileReader(fp_or_buf, **kwds) File "/120t/caix/anaconda3/envs/edta/lib/python3.6/site-packages/pandas/io/parsers.py", line 948, in init self._make_engine(self.engine) File "/120t/caix/anaconda3/envs/edta/lib/python3.6/site-packages/pandas/io/parsers.py", line 1180, in _make_engine self._engine = CParserWrapper(self.f, **self.options) File "/120t/caix/anaconda3/envs/edta/lib/python3.6/site-packages/pandas/io/parsers.py", line 2010, in init self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 540, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/120t/caix/anaconda3/envs/edta/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/120t/caix/anaconda3/envs/edta/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "/120t/caix/src/EDTA/test/EDTA-2.0.1/bin/TIR-Learner2.5/Module3/GetAllSeq.py", line 32, in GetListFromFile f=open(file,"r+") FileNotFoundError: [Errno 2] No such file or directory: 'TIR-Learner_FinalAnn.gff3' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/120t/caix/src/EDTA/test/EDTA-2.0.1/bin/TIR-Learner2.5/Module3/GetAllSeq.py", line 63, in pool.map(GetListFromFile,fileList) #shujun File "/120t/caix/anaconda3/envs/edta/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/120t/caix/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_FinalAnn.gff3' mv: 对 'TIR-Learner/FinalAnn.gff3' 调用 stat 失败: 没有那个文件或目录 mv: 对 'TIR-Learner/FinalAnn.fa' 调用 stat 失败: 没有那个文件或目录 Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: 没有那个文件或目录 at /120t/caix/src/EDTA/test/EDTA-2.0.1/util/rename_tirlearner.pl line 19. Warning: LOC list aa.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequenceCan't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: 没有那个文件或目录. Warning: The TIR result file has 0 bp!
2022年 07月 26日 星期二 22:29:26 CST Start to find Helitron candidates.
2022年 07月 26日 星期二 22:29:26 CST Identify Helitron candidates from scratch.
Warning: LOC list aa.fa.mod.HelitronScanner.raw.ext.list is empty. Warning: LOC list aa.fa.mod.HelitronScanner.raw.ext.list is empty.
Error: Error while loading sequence perl make_bed_with_intact.pl EDTA.intact.fa > EDTA.intact.bed
2022年 07月 26日 星期二 22:29:42 CST Warning: The Helitron result file has 0 bp!
2022年 07月 26日 星期二 22:29:42 CST Execution of EDTA_raw.pl is finished!
ERROR: Raw LTR results not found in aa.fa.mod.EDTA.raw/aa.fa.mod.LTR.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check
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