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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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trimming, fail? #184

Closed Ofsm closed 4 years ago

Ofsm commented 4 years ago

Hello, i'm working with some raw reads, trying to cut and clean adapters and I found this message ones it finished the work... someone have an idea about what is it... thanks

Here is the full entrance: (phyluce) name@namepc:~/uce-tutorial$ illumiprocessor \

--input raw-fastq/ \
--output clean-fastq \
--config illumiprocessor.conf \
--cores 2

2020-02-20 20:49:30,924 - illumiprocessor - INFO - ==================== Starting illumiprocessor =================== 2020-02-20 20:49:30,924 - illumiprocessor - INFO - Version: 2.0.9 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --config: illumiprocessor.conf 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --cores: 2 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --input: PATH/uce-tutorial/raw-fastq 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --log_path: None 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --min_len: 40 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --no_merge: False 2020-02-20 20:49:30,925 - illumiprocessor - INFO - Argument --output: PATH/uce-tutorial/clean-fastq 2020-02-20 20:49:30,926 - illumiprocessor - INFO - Argument --phred: phred33 2020-02-20 20:49:30,926 - illumiprocessor - INFO - Argument --r1_pattern: None 2020-02-20 20:49:30,926 - illumiprocessor - INFO - Argument --r2_pattern: None 2020-02-20 20:49:30,926 - illumiprocessor - INFO - Argument --se: False 2020-02-20 20:49:30,926 - illumiprocessor - INFO - Argument --trimmomatic: PATH/anaconda3/envs/phyluce/bin/trimmomatic 2020-02-20 20:49:30,926 - illumiprocessor - INFO - Argument --verbosity: INFO 2020-02-20 20:49:31,065 - illumiprocessor - INFO - Trimming samples with Trimmomatic Running......Traceback (most recent call last): File "PATH/anaconda3/envs/phyluce/bin/illumiprocessor", line 17, in sys.exit(main()) File "PATH/anaconda3/envs/phyluce/lib/python2.7/site-packages/illumiprocessor/cli/main.py", line 121, in main main(args) File "PATH/anaconda3/envs/phyluce/lib/python2.7/site-packages/illumiprocessor/main.py", line 45, in main pool.map(core.runner, work) File "/home/oscarsaenz/anaconda3/envs/phyluce/lib/python2.7/multiprocessing/pool.py", line 253, in map return self.map_async(func, iterable, chunksize).get() File "PATH/anaconda3/envs/phyluce/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value OSError: [Errno 2] No such file or directory