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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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bulidMatrix error #324

Closed hzaumsq closed 5 years ago

hzaumsq commented 5 years ago

when I use a big sam/bam(20G~30G) file after bowtie2 or bwa , It seemed meet a mistake. The error information as follow ! The command I used ##：hicBuildMatrix --samFiles WHF4-1Hi-C_R1.sam WHF4-1Hi-C_R2.sam --binSize 40000 --restrictionSequence GATC --outFileName 40k.h5 --outBam WHF4-1Hi-C_40k.bam --QCfolder ./QC --threads 20 --inputBufferSize 400000 ###

Traceback (most recent call last): File "/public/home/dxbo/miniconda3/bin/hicBuildMatrix", line 7, in main() File "/public/home/dxbo/miniconda3/lib/python3.6/site-packages/hicexplorer/hicBuildMatrix.py", line 1247, in main process[i].start() File "/public/home/dxbo/miniconda3/lib/python3.6/multiprocessing/process.py", line 105, in start self._popen = self._Popen(self) File "/public/home/dxbo/miniconda3/lib/python3.6/multiprocessing/context.py", line 223, in _Popen return _default_context.get_context().Process._Popen(process_obj) File "/public/home/dxbo/miniconda3/lib/python3.6/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/public/home/dxbo/miniconda3/lib/python3.6/multiprocessing/popen_fork.py", line 19, in init self._launch(process_obj) File "/public/home/dxbo/miniconda3/lib/python3.6/multiprocessing/popen_fork.py", line 66, in _launch self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory

joachimwolff commented 5 years ago

Hi,

You run out of memory. What you can try is to reduce the number of cores, in my experience it is not giving a benefit to use more than 6 cores. Otherwise you need to split the bam files and build two or three smaller matrices and merge them afterwards. However the simplest solution is to run the jobs on a machine with more memory. If you don’t have access to more resources I can recommend hicexplorer.usegalaxy.eu.

Best,

Joachim

hzaumsq commented 5 years ago

OK，I‘have solved this problem by taking your advise.That's very kind of you.