dhrititandon
commented
5 years ago I forgot to mention that in my log file I get the following error
Traceback (most recent call last): File "/home/dtandon/.conda/envs/hitad/bin/hitad", line 121, in run G.learning(cpu_core=args.cpu_core) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/tadlib/hitad/genomeLev.py", line 199, in learning seqs = self.train_data(res, rep) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/tadlib/hitad/genomeLev.py", line 176, in train_data tmpcache.calDI(tmpcache.windows, 0) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/tadlib/hitad/chromLev.py", line 356, in calDI lthre = np.percentile(self.DIs[self.DIs<0], 0.1) File "<__array_function__ internals>", line 6, in percentile File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/numpy/lib/function_base.py", line 3713, in percentile a, q, axis, out, overwrite_input, interpolation, keepdims) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/numpy/lib/function_base.py", line 3833, in _quantile_unchecked interpolation=interpolation) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/numpy/lib/function_base.py", line 3410, in _ureduce r = func(a, kwargs) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/numpy/lib/function_base.py", line 3948, in _quantile_ureduce_func x1 = take(ap, indices_below, axis=axis) weights_below File "<__array_function__ internals>", line 6, in take File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 194, in take return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode) File "/home/dtandon/.conda/envs/hitad/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 61, in _wrapfunc return bound(args, kwds) IndexError: cannot do a non-empty take from an empty axes.
AyushSemwal
rachadele
Upon running hitad, I get the following text. My input command is [ hitad --output test_50000.txt -d meta_file_50kb --logFile hitad.log ]. Although the prompt gives a 'done' message, there is no output file and I don't think that the program even proceeds with the TAD parsing.
root INFO @ 10/17/19 18:16:14:
ARGUMENT LIST:
Output file name = test_50000.txt
Hi-C datasets = {500000: {'rep1': '/scratch/network/dtandon/HiCLiver2/SRR17.output_50000.cool'}}
Column for matrix balancing = weight
Excluded chromosomes = ['chrY', 'chrM']
Maximum domain size = 4000000
Column for DI track = DIs
Number of processes used = 1
Remove cache data = False
Log file name = hitad.log
root INFO @ 10/17/19 18:16:16: Parsing Hi-C datasets ... root INFO @ 10/17/19 21:01:05: Done!