A problem with the number of files (Python)

Question

A problem with the number of files (Python)

andreyurch opened this issue 8 years ago · 5 comments

Traceback (most recent call last):
File "/export/home/aay2c/app2/DBG2OLC-master/utility/split_reads_by_backbone.py", line 131, in
File "/export/home/aay2c/app2/DBG2OLC-master/utility/split_reads_by_backbone.py", line 122, in main
IOError: [Errno 24] Too many open files: './consensus_dir/backbone-2778.reads.fasta'

Answer 1 · 2017-04-05T23:21:19.000Z

We need to open a lot of files to distribute the above file into lots of smaller files so please make sure you have the privilege to run:
ulimit -n unlimited

Answer 2 · 2017-04-06T12:41:03.000Z

Thank you for the answer, but I found that: it is almost impossible to modify this parameter on the Mac OS starting from El Captain. I and many other potential users of the DBG2OLC do not have the root privileges to modify ulimit on the Linux systems. So, I am completely stacked at this point, while the backbone assembly is perfect...

Answer 3 · 2017-04-06T16:42:08.000Z

I see. Please take a look at other forks of DBG2OLC and see if their correction works. If so, please let me know and I would try to merge them.

For example:
https://github.com/JohnUrban/DBG2OLC

Answer 4 · 2017-04-19T12:52:29.000Z

Hello, Yes I have finished successfully with https://github.com/JohnUrban/DBG2OLC/tree/split_reads_by_backbone_minimize_open_files/utility

Answer 5 · 2017-04-20T16:03:40.000Z

Cool. Thanks for the feedback!