Hello, thank you all for developing SCI which is really innovative in Hi-C research.
This error occured when I used SCI to analyze resolution=10000 hg19-annotated GM12878 HIC001 matrix (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1551550). But I have successfully analyzed resolution=40000-mm10 annotated HIC matrix.
My cluster server has rather large memory, and I noticed that this error pops up whatever the size of
input file. I suppose the reason is resolution=10000 is too high for SCI.
Here is the error.
################################################################
writing HiC graph: 100%|##########| 231/231 [8:00:33<00:00, 124.82s/it]
['/home/user/software/sci-master/LINE/line', '-train', 'test_HiC_graph.txt', '-order', '1', '-samples', '1', '-output', 'test_HiC_graph_order_1_samples_1M.embedding']
Traceback (most recent call last):
File "/home/user/software/sci-master/sci/sci.py", line 113, in
run_sci()
File "/home/user/software/sci-master/sci/sci.py", line 109, in run_sci
oArgs.clusters)
File "/home/user/software/sci-master/sci/Compartments.py", line 32, in predict_subcompartents
embedding_files = run_LINE(graphFile, samples, order)
File "/home/user/software/sci-master/sci/utils.py", line 63, in run_LINE
tOutput = _LaunchJob(command)
File "/home/user/software/sci-master/sci/utils.py", line 23, in _LaunchJob
stderr=subprocess.PIPE)
File "/home/user/miniconda2/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/home/user/miniconda2/lib/python2.7/subprocess.py", line 938, in _execute_child
self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory
Hello, thank you all for developing SCI which is really innovative in Hi-C research.
This error occured when I used SCI to analyze resolution=10000 hg19-annotated GM12878 HIC001 matrix (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1551550). But I have successfully analyzed resolution=40000-mm10 annotated HIC matrix.
My cluster server has rather large memory, and I noticed that this error pops up whatever the size of
input file. I suppose the reason is resolution=10000 is too high for SCI.
Here is the error.
################################################################
writing HiC graph: 100%|##########| 231/231 [8:00:33<00:00, 124.82s/it]
['/home/user/software/sci-master/LINE/line', '-train', 'test_HiC_graph.txt', '-order', '1', '-samples', '1', '-output', 'test_HiC_graph_order_1_samples_1M.embedding']
Traceback (most recent call last):
File "/home/user/software/sci-master/sci/sci.py", line 113, in
run_sci()
File "/home/user/software/sci-master/sci/sci.py", line 109, in run_sci
oArgs.clusters)
File "/home/user/software/sci-master/sci/Compartments.py", line 32, in predict_subcompartents
embedding_files = run_LINE(graphFile, samples, order)
File "/home/user/software/sci-master/sci/utils.py", line 63, in run_LINE
tOutput = _LaunchJob(command)
File "/home/user/software/sci-master/sci/utils.py", line 23, in _LaunchJob
stderr=subprocess.PIPE)
File "/home/user/miniconda2/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/home/user/miniconda2/lib/python2.7/subprocess.py", line 938, in _execute_child
self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory