Memory error for large datasets

[jf2016GH]

$time python nclist.py

Subject file: chainOrnAna1.bed (1.956864), Query file: chainRn4.bed (2.350965)
Building NCLS took 0.36449146270751953
Traceback (most recent call last):
File "nclist.py", line 36, in
time_ncls(s, q)
File "nclist.py", line 22, in time_ncls
n.all_overlaps_both(q[1].values, q[2].values, q.index.values)
File "ncls/src/ncls.pyx", line 278, in ncls.src.ncls.NCLS.all_overlaps_both
File "ncls/src/ncls.pyx", line 321, in ncls.src.ncls.NCLS.all_overlaps_both
File "/home/john/anaconda3/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 1320, in resize
a = concatenate((a,) * n_copies)
MemoryError

[endrebak]

Thanks. This happens when the number of enumerated intervals is very large. I’ll have a look :)

[endrebak]

While I cannot do anything to prevent this from happening, I can write a user-friendly error message instead. I will do that :)

If this means that the NCLS fails on large data where the AIList this is a very interesting result for me :)

[jf2016GH]

AIList for python is updated. It is close to c-code in speed. On Tuesday, November 12, 2019, 9:44:53 AM EST, Endre Bakken Stovner <[email protected]> wrote: While I cannot do anything to prevent this from happening, I can write a user-friendly error message instead. I will do that :) If this means that the NCLS fails on large data where the AIList this is a very interesting result for me :) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.