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Cannot allocate memory #186

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wlaw13 opened this issue Oct 28, 2019 · 0 comments
Open

Cannot allocate memory #186

wlaw13 opened this issue Oct 28, 2019 · 0 comments

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@wlaw13
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wlaw13 commented Oct 28, 2019

Hello,

I'm trying to use the poretools combine utility across 10 different replicates. It worked perfect for 9 of the 10, but the last one is throwing an odd error:

Traceback (most recent call last):
File "/work-zfs/amccall2/WDL/Nanopore_Test_Data/poretools/poretools/poretools_main.py", line 544, in
main()
File "/work-zfs/amccall2/WDL/Nanopore_Test_Data/poretools/poretools/poretools_main.py", line 538, in main
args.func(parser, args)
File "/work-zfs/amccall2/WDL/Nanopore_Test_Data/poretools/poretools/poretools_main.py", line 55, in run_subtool
submodule.run(parser, args)
File "/work-zfs/amccall2/WDL/Nanopore_Test_Data/poretools/poretools/combine.py", line 24, in run
tar.add(fast5.filename)
File "/software/apps/anaconda/5.2/python/2.7/lib/python2.7/tarfile.py", line 2025, in add
self.addfile(tarinfo, f)
File "/software/apps/anaconda/5.2/python/2.7/lib/python2.7/tarfile.py", line 2054, in addfile
copyfileobj(fileobj, self.fileobj, tarinfo.size)
File "/software/apps/anaconda/5.2/python/2.7/lib/python2.7/tarfile.py", line 275, in copyfileobj
dst.write(buf)
File "/software/apps/anaconda/5.2/python/2.7/lib/python2.7/gzip.py", line 241, in write
self.fileobj.write(self.compress.compress(data))
IOError: [Errno 12] Cannot allocate memory

I assume it was simply a memory problem, but the server claims it isn't using very much memory at all. I tried rerunning it and giving it 50Gb of RAM, but it still failed and threw the same error.

Any suggestions?

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