Program error with output

[dhrititandon]

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!

[dhrititandon]

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]

I am also having the same issue. Were you able to figure out?

[rachadele]

Nope. I ended up using Juicer tools to generate a matrix and call TADs. Works much better!

…

On Sun, Dec 15, 2019 at 5:05 PM AyushSemwal ***@***.***> wrote: I am also having the same issue. Were you able to figure out? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#12?email_source=notifications&email_token=AMIA3ITZ2L6RZVSEZ3C5SGTQY3H43A5CNFSM4JCJCJCKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEG5HLFI#issuecomment-565867925>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMIA3IQU4NTWW4JXVSETFVLQY3H43ANCNFSM4JCJCJCA> .