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zhpn1024 / ribotish

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
http://dx.doi.org/10.1038/s41467-017-01981-8
GNU General Public License v3.0
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Error running ribotish predict with multicore parameters #3

Closed elabaronne closed 2 years ago

elabaronne commented 5 years ago

Hi, I'm trying to use the whole pipeline of ribotish. When I run the command ribotish predict -t unassigned_HARR_mapped_sort.bam -b unassigned_mapped_sort.bam -g ../gencode/gencode.v28.annotation_appris_princ_1.gtf -f ../gencode/GRCh38.p12.genome.fa -o unassigned_pred.txt -p 8 i get this error : Thu Jun 27 17:21:06 2019 Estimating TIS background parameters... Traceback (most recent call last): File "/home/adminmanu/softwares/miniconda3/bin/ribotish", line 56, in <module> main() File "/home/adminmanu/softwares/miniconda3/bin/ribotish", line 34, in main commands[cmd].run(args) File "/home/adminmanu/softwares/miniconda3/lib/python3.7/site-packages/ribotish/run/predict.py", line 151, in run pool = MyPool(1) # This is for memory efficiency File "/home/adminmanu/softwares/miniconda3/lib/python3.7/multiprocessing/pool.py", line 177, in __init__ self._repopulate_pool() File "/home/adminmanu/softwares/miniconda3/lib/python3.7/multiprocessing/pool.py", line 238, in _repopulate_pool self._wrap_exception) File "/home/adminmanu/softwares/miniconda3/lib/python3.7/multiprocessing/pool.py", line 252, in _repopulate_pool_static wrap_exception) File "/home/adminmanu/softwares/miniconda3/lib/python3.7/multiprocessing/process.py", line 74, in __init__ assert group is None, 'group argument must be None for now' AssertionError: group argument must be None for now

This error did not occur when I use the same command without the -p parameters so I can continue with downstream analysis using one core.

I'm using ribotish with python 3.7

Thanks

zhpn1024 commented 5 years ago

It may be a problem only in the new version of python. I will check it. The error may only occur when generating .bgest.txt file using multiprocessing. If you have already generated the .bgest.txt background file using one CPU, this step will be skipped, and you may use multiprocessing without error.

zhpn1024 commented 5 years ago

The error is probably because your multiprocessing module is not up-to-date for python 3.7.