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YaqiangCao / cLoops

Accurate and flexible loops calling tool for 3D genomic data.
https://yaqiangcao.github.io/cLoops/
MIT License
109 stars 17 forks source link

callstripes has problems #4

Closed MackZhang closed 5 years ago

MackZhang commented 6 years ago

I can not set parameters except default ones. The callstripe program will report an error even the default parameter, like "-minPts 5", appear on the command line.

MackZhang commented 6 years ago

callStripes -d CTCF_HiChIP -o CTCF_stripe -c chr21 -j 2018-11-15 20:45:16,118 INFO Command line: callStripes -d CTCF_HiChIP -o CTCF_stripe -eps 20000 -minPts 5 -pets 200 -ext 50 -c ['chr21'] -p 1 -j True Clustering chr21 and chr21 using eps as 20000, minPts as 5 Clustering chr21 and chr21 finished. Clustering chr21 and chr21 using eps as 20000, minPts as 5 Clustering chr21 and chr21 finished. Genomic coverage model built from CTCF_HiChIP/chr21-chr21.jd 0 interaction p-values estimated for CTCF_HiChIP/chr21-chr21.jd Genomic coverage model built from CTCF_HiChIP/chr21-chr21.jd 0 interaction p-values estimated for CTCF_HiChIP/chr21-chr21.jd 2018-11-15 20:46:00,516 INFO callStripes finished. Bye! Used time:0:00:44.399089

callStripes -d CTCF_HiChIP -o CTCF_stripe -c chr21 -j -minPts 5 2018-11-15 20:46:08,362 INFO Command line: callStripes -d CTCF_HiChIP -o CTCF_stripe -eps 20000 -minPts 5 -pets 200 -ext 50 -c ['chr21'] -p 1 -j True Clustering chr21 and chr21 using eps as 20000, minPts as 5 Clustering chr21 and chr21 finished. Clustering chr21 and chr21 using eps as 20000, minPts as 5 Clustering chr21 and chr21 finished. Genomic coverage model built from CTCF_HiChIP/chr21-chr21.jd

Traceback (most recent call last): File "/usr/local/bin/callStripes", line 5, in pkg_resources.run_script('cLoops==0.91', 'callStripes') File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.35-py2.7.egg/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.35-py2.7.egg/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/usr/local/lib/python2.7/dist-packages/cLoops-0.91-py2.7.egg/EGG-INFO/scripts/callStripes", line 472, in cpus=op.cpu) File "/usr/local/lib/python2.7/dist-packages/cLoops-0.91-py2.7.egg/EGG-INFO/scripts/callStripes", line 348, in callStripes ds_x = pd.concat(ds_x) File "/usr/local/lib/python2.7/dist-packages/pandas/core/reshape/concat.py", line 225, in concat copy=copy, sort=sort) File "/usr/local/lib/python2.7/dist-packages/pandas/core/reshape/concat.py", line 277, in init raise ValueError('All objects passed were None') ValueError: All objects passed were None

YaqiangCao commented 6 years ago

Hi Mack, Sorry for the bug. Could you please give us some sample of the data you used? Such as the chr21. We will try to tune the parameters for you. We initially tune the parameters for H3K27ac HiChIP, so it may be not suitable for your data. We will try to fix the parameter problem. Best, Yaqiang & Zhaoxiong

MackZhang commented 6 years ago

I download CTCF HiChIP data form GEO, and the access number is: GSM2705060,GSM2705061.

YaqiangCao commented 6 years ago

Could you please give us the bedpe for the data of chr21. It will take long time for us to download and pre-processing and fix the bug for you.