Error return without exception set - Githubissues

XiaoTaoWang / TADLib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

GNU General Public License v3.0

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Error return without exception set #2

Closed laraib85 closed 7 years ago

laraib85 commented 7 years ago

Hi,

I tried running the tool on processed Hi-C data from the Rao et al paper with the KR normalization method. However, each time I get the following error:

root                      INFO    @ 11/05/17 17:06:49: Parsing Hi-C datasets ...
tadlib.hitad.genomeLev    DEBUG   @ 11/05/17 17:06:49: Chrom 1:
tadlib.hitad.genomeLev    DEBUG   @ 11/05/17 17:06:49:   resolution: 500000, rep1
tadlib.hitad.genomeLev    DEBUG   @ 11/05/17 17:06:53:   Cache Chrom object into /home/laraib/.hitad/tmpmoCZ8T20171105170653 ...
Traceback (most recent call last):
  File "/home/laraib/miniconda2/bin/hitad", line 119, in run
    G = Genome(args.datasets, args.chroms, args.maxsize, args.npzpre, cachefolder)
  File "/home/laraib/miniconda2/lib/python2.7/site-packages/tadlib/hitad/genomeLev.py", line 160, in __init__
    cPickle.dump(work, output, protocol = 2)
SystemError: error return without exception set

I tried multiple resolutions as well, ranging from 5kb to 500kb but to no avail.

XiaoTaoWang commented 7 years ago

Can you show me your input Hi-C data (with linux head command)?

laraib85 commented 7 years ago

Sure, here is one of them (the columns are tab-delimited):

6027    6283    2.0955317252
16674   16713   1.28669960457
21722   22631   5.54419196153
535     3421    14.9422995601
11675   11884   5.03226812195
23163   24634   8.58252500088
20091   20461   4.78734712728
19762   23175   20.3328842376
1132    1407    2.02352411334
17299   23011   25.4211912422

XiaoTaoWang commented 7 years ago

And did you get the same error when followed the tutorial (http://xiaotaowang.github.io/TADLib/hitad.html) with those example data on your system?

XiaoTaoWang commented 7 years ago

And the version of your python and scipy?

laraib85 commented 7 years ago

It runs on the example data but crashes while parsing my input data. Scipy version 0.18.1.

XiaoTaoWang commented 7 years ago

That error seems to be related to this issue (http://bugs.python.org/issue11564), that is, cPickle has trouble in dumping large objects. However, I think it doesn't explain your case, at least for low-resolution inputs. Would you mind emailing your input data on 500Kb to me (wangxiaotao868@163.com)?

XiaoTaoWang commented 7 years ago

Hey, the head of your "chr1.txt" is shown below::

120.54 125.66 2.0955317252
333.48 334.26 1.28669960457
434.44 452.62 5.54419196153
10.7 68.42 14.9422995601
233.5 237.68 5.03226812195
463.26 492.68 8.58252500088
401.82 409.22 4.78734712728
395.24 463.5 20.3328842376
22.64 28.14 2.02352411334

I think the float type of the first two columns could explain the weird error.

laraib85 commented 7 years ago

Oh yeah. I mixed up the resolution of some files and ended up doing that! I just tried the tool on the 5k data to cross-check. Works well. Thanks!