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.
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?