Hello!
I am facing two problems while running neoloopfinder
1) when I run segment-cnv I continue to get this error with most of my cool matrix at different resolutions:
ARGUMENT LIST:
CNV Profile = /gpfs/data/HernandoLab/home/bericp01/HiC/results/CNV/501mel_sgCHD7-2_NeoLoopFinder/501mel_sgCHD7-2_25k.CNV-profile.bedGraph
Number of States = None
CBS P-value Cutoff = 1e-05
Maximum HMM-CBS distance = 4
Minimum Copy Number difference = 0.4
Minimum Segment Size = 3
Ploidy = 2
Bin Size = 25000
Output Path = /gpfs/data/HernandoLab/home/bericp01/HiC/results/CNV/501mel_sgCHD7-2_NeoLoopFinder/501mel_sgCHD7-2_25k.CNV-seg.bedGraph
Number of Processes = 10
Log file name = cnv-seg.log
root INFO @ 04/26/24 18:51:53: Loading CNV profile ...
neoloop.cnv.segcnv INFO @ 04/26/24 18:51:54: Training HMM with 3 states...
Traceback (most recent call last):
File "/gpfs/data/HernandoLab/home/bericp01/miniconda_bericp01/envs/NeoLoopFinder/bin/segment-cnv", line 111, in run
work.segment(
File "/gpfs/data/HernandoLab/home/bericp01/miniconda_bericp01/envs/NeoLoopFinder/lib/python3.10/site-packages/neoloop/cnv/segcnv.py", line 167, in segment
model = HiddenMarkovModel.from_samples(
File "pomegranate/hmm.pyx", line 3705, in pomegranate.hmm.HiddenMarkovModel.from_samples
ValueError: need at least one array to concatenate
2) all my plots are not centered to the 0 but rather always below zero irrespective if are cancer or normal cells. Any clue?
Any help will be really appreciate!!!
Thanks
Pietro
Hello! I am facing two problems while running neoloopfinder 1) when I run segment-cnv I continue to get this error with most of my cool matrix at different resolutions:
ARGUMENT LIST: CNV Profile = /gpfs/data/HernandoLab/home/bericp01/HiC/results/CNV/501mel_sgCHD7-2_NeoLoopFinder/501mel_sgCHD7-2_25k.CNV-profile.bedGraph Number of States = None CBS P-value Cutoff = 1e-05 Maximum HMM-CBS distance = 4 Minimum Copy Number difference = 0.4 Minimum Segment Size = 3 Ploidy = 2 Bin Size = 25000 Output Path = /gpfs/data/HernandoLab/home/bericp01/HiC/results/CNV/501mel_sgCHD7-2_NeoLoopFinder/501mel_sgCHD7-2_25k.CNV-seg.bedGraph Number of Processes = 10 Log file name = cnv-seg.log root INFO @ 04/26/24 18:51:53: Loading CNV profile ... neoloop.cnv.segcnv INFO @ 04/26/24 18:51:54: Training HMM with 3 states... Traceback (most recent call last): File "/gpfs/data/HernandoLab/home/bericp01/miniconda_bericp01/envs/NeoLoopFinder/bin/segment-cnv", line 111, in run work.segment( File "/gpfs/data/HernandoLab/home/bericp01/miniconda_bericp01/envs/NeoLoopFinder/lib/python3.10/site-packages/neoloop/cnv/segcnv.py", line 167, in segment model = HiddenMarkovModel.from_samples( File "pomegranate/hmm.pyx", line 3705, in pomegranate.hmm.HiddenMarkovModel.from_samples ValueError: need at least one array to concatenate
2) all my plots are not centered to the 0 but rather always below zero irrespective if are cancer or normal cells. Any clue?
Any help will be really appreciate!!! Thanks Pietro