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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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sre_constants.error: nothing to repeat #134

Closed discipleofdarwin closed 5 years ago

discipleofdarwin commented 5 years ago

Hi Dr. Faircloth,

I do not know what happened, all of a sudden the illumiprocessor stopped working and I received this error message. Here below is the entire output, also my conda list illumiprocessor shows the 2.0.8 version below you can see it says 2.0.6 when the program runs.

illumiprocessor --input raw2/ --output clean-fastq --config illumiprocessor.conf --trimmomatic /home/charles/anaconda2/envs/illumiprocessor/jar/trimmomatic.jar --r1-pattern _R1 --r2-pattern _R2 2018-11-06 23:00:56,398 - illumiprocessor - INFO - ==================== Starting illumiprocessor =================== 2018-11-06 23:00:56,399 - illumiprocessor - INFO - Version: 2.0.6 2018-11-06 23:00:56,399 - illumiprocessor - INFO - Argument --config: illumiprocessor.conf 2018-11-06 23:00:56,399 - illumiprocessor - INFO - Argument --cores: 1 2018-11-06 23:00:56,400 - illumiprocessor - INFO - Argument --input: /home/charles/Dropbox/Actual/raw2 2018-11-06 23:00:56,400 - illumiprocessor - INFO - Argument --log_path: None 2018-11-06 23:00:56,400 - illumiprocessor - INFO - Argument --min_len: 40 2018-11-06 23:00:56,401 - illumiprocessor - INFO - Argument --no_merge: False 2018-11-06 23:00:56,401 - illumiprocessor - INFO - Argument --output: /home/charles/Dropbox/Actual/clean-fastq 2018-11-06 23:00:56,401 - illumiprocessor - INFO - Argument --phred: phred33 2018-11-06 23:00:56,401 - illumiprocessor - INFO - Argument --r1_pattern: _R1 2018-11-06 23:00:56,401 - illumiprocessor - INFO - Argument --r2_pattern: _R2 2018-11-06 23:00:56,402 - illumiprocessor - INFO - Argument --se: False 2018-11-06 23:00:56,402 - illumiprocessor - INFO - Argument --trimmomatic: /home/charles/anaconda2/envs/illumiprocessor/jar/trimmomatic.jar 2018-11-06 23:00:56,403 - illumiprocessor - INFO - Argument --verbosity: INFO Traceback (most recent call last): File "/home/charles/anaconda2/envs/illumiprocessor/bin/illumiprocessor", line 17, in sys.exit(main()) File "/home/charles/anaconda2/envs/illumiprocessor/lib/python2.7/site-packages/illumiprocessor/cli/main.py", line 131, in main main(args) File "/home/charles/anaconda2/envs/illumiprocessor/lib/python2.7/site-packages/illumiprocessor/main.py", line 34, in main reads.append(core.SequenceData(args, conf, start_name, end_name)) File "/home/charles/anaconda2/envs/illumiprocessor/lib/python2.7/site-packages/illumiprocessor/core.py", line 86, in init self._get_read_data() File "/home/charles/anaconda2/envs/illumiprocessor/lib/python2.7/site-packages/illumiprocessor/core.py", line 97, in _get_read_data if re.search(self.r1_pattern.format(self.start_name), name): File "/home/charles/anaconda2/envs/illumiprocessor/lib/python2.7/re.py", line 146, in search return _compile(pattern, flags).search(string) File "/home/charles/anaconda2/envs/illumiprocessor/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression sre_constants.error: nothing to repeat

brantfaircloth commented 5 years ago

It looks like the regular expression pattern that you are passing is not correct (you need to pass a valid regular expression to match your R1 and R2 file names).

discipleofdarwin commented 5 years ago

Hi Dr.Faircloth,

Thank you very much for the assistance, I figured out the problem. The problem is that I did not put '.' in front of in the --r1-pattern _R1 --r2-pattern _R2 line. When changed to --r1-pattern ._R1 --r2-pattern ._R2 things work just fine.