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khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics
http://www.recentrifuge.org
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Bug Report: PermissionError: [Errno 13] Permission denied #24

Closed hansir8 closed 4 years ago

hansir8 commented 4 years ago

Here is the bug report of recentrifuge. The error is list below: --------> =-= /home/Software/Miniconda3/envs/poliolab-ngs-env/bin/rcf =-= v1.1.0 - Jun 2020 =-= by Jose M anuel Martí =-=

Loading NCBI nodes... OK! Loading NCBI names... OK! Building dict of parent to children taxa... OK!

Please, wait, processing files in parallel...

Traceback (most recent call last): File "/home/Software/Miniconda3/envs/poliolab-ngs-env/bin/rcf", line 836, in main() File "/home/Software/Miniconda3/envs/poliolab-ngs-env/bin/rcf", line 795, in main read_samples() File "/home/Software/Miniconda3/envs/poliolab-ngs-env/bin/rcf", line 461, in read_samples len(input_files))) as pool: File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/pool.py", line 156, in init self._setup_queues() File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/pool.py", line 249, in _setup_queues self._inqueue = self._ctx.SimpleQueue() File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/context.py", line 112, in SimpleQueue return SimpleQueue(ctx=self.get_context()) File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/queues.py", line 315, in init self._rlock = ctx.Lock() File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/context.py", line 67, in Lock return Lock(ctx=self.get_context()) File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/synchronize.py", line 162, in init SemLock.init(self, SEMAPHORE, 1, 1, ctx=ctx) File "/home/Software/Miniconda3/envs/poliolab-ngs-env/lib/python3.6/multiprocessing/synchronize.py", line 59, in init unlink_now) PermissionError: [Errno 13] Permission denied ----------->

The command line is: --------> rcf -n /Database/taxdump/ -k 03.Reads.classify/kraken2_classification_result -e FULL -o 03.Reads.classify/classification.kraken2.html --------->

I have test the version v1.1.0 and v1.1.1, and all appear this error. Can you provide a solution for this ?

khyox commented 4 years ago

The PermissionError exception is quite self-explanatory and it usually is raised in that part of the code if you have not read permissions on the directory or the files you are trying to read. Please check that you have the proper permissions on the 03.Reads.classify/kraken2_classification_result directory. To check it, you can issue a ls -l 03.Reads.classify/kraken2_classification_result command and check the output.

hansir8 commented 4 years ago

Thanks for your quick reply! I have tried this solution using the command line. ------> chmod -R 755 03.Reads.classify/ -------> However, I also meet this problem using the common user. When I used the root user, the problem was solved successfully. I speculated that the conda environment permission could caused this question. Thanks very much for your help again!

Zhenzhi Han

khyox commented 4 years ago

Thanks for the feedback, Zhenzhi! I am glad that you could solve that issue. It seems very specific to the bioconda environment. Enjoy recentrifuge!