colinliuzelin
commented
2 years ago Hi, Thank you for your question. I think your issue was raised by the wrong module 'intervals'. There are a lot of python packages named intervals in the environment. I suggest you first uninstall any module named intervals (such as intervals, pyinterval) or create a new conda environment. Please intall python-intervals with 'pip install python-intervals'. You can type "import intervals as I; I.empty()" to test it. Best, Zelin
bredward
Hi there,
I keep having an issue with circfull RG not running to completion. It seems to be related to multiprocessing however the error still occurs when I reduce the # of threads. I've done a little research to see if it's something I can resolve myself but I have not found a reasonable explanation for what could be causing the problem. If you have any thoughts on how to troubleshoot this (see log pasted below) or if this looks at all familiar, your advice would be greatly appreciated!
For reference, here is the log during the running process and the specific error that I'm getting at the bottom. I should also note that I've tried setting the # threads lower (< the default) and that doesn't seem to make a difference. I've also tried splitting the fastq input into smaller files and it doesn't seem to help either - I see the error message regardless.
2022-06-01 11:33:36
Check fastq file
2022-06-01 11:33:36
Check anno file
2022-06-01 11:33:36
Check genome file
2022-06-01 11:33:36
Align fastq to reference genome: alignFastq
2022-06-01 12:22:14
Transform SAM to BAM: sam2bam
2022-06-01 12:22:17
Analyze SAM file: explainFL
2022-06-01 12:22:36
Filter and classify candidates: filterFL
2022-06-01 12:22:43 #### |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | ETA: 0:00:00
Adjust normal: adjExplainNormal multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/site-packages/circfull-0.0.8-py3.9.egg/circfull/RG_adjExplainNormal.py", line 30, in getNewFL exon1=createIntervals(each1['exon_start'],each1['exon_end']) File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/site-packages/circfull-0.0.8-py3.9.egg/circfull/RG_adjExplainNormal.py", line 7, in createIntervals x=I.empty() AttributeError: module 'intervals' has no attribute 'empty' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/bredward/miniconda3/envs/circfull/bin/circfull", line 33, in
sys.exit(load_entry_point('circfull==0.0.8', 'console_scripts', 'circfull')())
File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/site-packages/circfull-0.0.8-py3.9.egg/circfull/circFL_main.py", line 37, in main
File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/site-packages/circfull-0.0.8-py3.9.egg/circfull/RG.py", line 87, in RG
File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/site-packages/circfull-0.0.8-py3.9.egg/circfull/RG_adjExplainNormal.py", line 60, in adjExplainNormal
File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/bredward/miniconda3/envs/circfull/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
AttributeError: module 'intervals' has no attribute 'empty'
Again, I appreciate your help with this. I am looking forward to utilizing the full pipeline as soon as I am able to resolve this!
-Bri Edwards