yaqiangcao / cloops2 Goto Github PK

Hi,

I tried to install cLoops2 from source for latest version:

$ conda create -n cLoops2-2 python=3.7
$ conda activate cLoops2-2
$ conda env update --file cLoops2_env.yaml

It shows errors:

Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: / Ran pip subprocess with arguments:
['/home/mypath/anaconda3/envs/cLoops2-2/bin/python', '-m', 'pip', 'install', '-U', '-r', '/scr1/users/mypath/Software2/cLoops2/condaenv.emnigv1o.requirements.txt', '--exists-action=b']
Pip subprocess output:

Pip subprocess error:
ERROR: Could not find a version that satisfies the requirement cloops2==1.0.0 (from -r /scr1/users/mypath/Software2/cLoops2/condaenv.emnigv1o.requirements.txt (line 1)) (from versions: 0.0.2, 0.0.3)
ERROR: No matching distribution found for cloops2==1.0.0 (from -r /scr1/users/mypath/Software2/cLoops2/condaenv.emnigv1o.requirements.txt (line 1))

failed

CondaEnvException: Pip failed

I then tried to install cLoops2 directly from pip:
$ conda deactivate
$ pip install cLoops2
It says:
Successfully installed cLoops2-0.0.3 pyBigWig-0.3.22

But when I run $ cLoops2
It shows error:

Traceback (most recent call last):
File "/cm/shared/easybuild/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/init.py", line 23, in
from . import multiarray
File "/cm/shared/easybuild/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/multiarray.py", line 10, in
from . import overrides
File "/cm/shared/easybuild/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/overrides.py", line 6, in
from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/mypath/anaconda3/bin/cLoops2", line 5, in
from cLoops2.cLoops2 import main
File "/home/mypath/anaconda3/lib/python3.9/site-packages/cLoops2/cLoops2.py", line 25, in
import numpy as np
File "/cm/shared/easybuild/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/init.py", line 144, in
from . import core
File "/cm/shared/easybuild/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/init.py", line 49, in
raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

• The Python version is: Python3.9 from "/home/mypath/anaconda3/bin/python"
• The NumPy version is: "1.22.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath'

Looking forward to your reply!

Thanks!

Best,
Charles

Hi,
When I run cLoop2 to call loops, it worked for some chromosomes, but failed at last.

some output:

2023-03-17 12:33:02,069 INFO Clustering chr22_KI270738v1_random and chr22_KI270738v1_random using eps 500, minPts 10,pre-set distance cutoff > 841
2023-03-17 12:33:02,212 INFO Clustering chr22_KI270738v1_random and chr22_KI270738v1_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.

The errors are as follows, is there anything wrong in my script? Thanks.

tc=k562_hitrac
cLoops2 callLoops -d $tc -o $tc  -eps 200,500,1000,2000 -minPts 10 -max_cut -w -j

errors:
report = "No PETs found in %s, maybe due to cut > %" % (fixy, cut)
ValueError: incomplete format

Same issue as described here:
allind/EukDetect#8

Hello Dr Gao,

Thanks for your help in advance. When I tried with montage command it shows errors with example data:

cLoops2 montage -f k562_bio1/chr21-chr21.ixy -bed runx1.bed -o test
2023-04-07 18:34:09,585 INFO Command cLoops2 montage -f k562_bio1/chr21-chr21.ixy -bed runx1.bed -ext 2 -o test -cut 0 -mcut -1 -simple False -viewPoint -vmin None -vmax None -ppmw 10 -aw 1 -no1D False
Traceback (most recent call last):
File "path/cLoops2/bin/cLoops2", line 33, in
sys.exit(load_entry_point('cLoops2==0.0.4', 'console_scripts', 'cLoops2')())
File "path/cLoops2/lib/python3.7/site-packages/cLoops2-0.0.4-py3.7.egg/cLoops2/cLoops2.py", line 4133, in main
oneD=oneD,
File "path/cLoops2/lib/python3.7/site-packages/cLoops2-0.0.4-py3.7.egg/cLoops2/montage.py", line 535, in montage
label=label)
File "path/cLoops2/lib/python3.7/site-packages/cLoops2-0.0.4-py3.7.egg/cLoops2/montage.py", line 232, in fill_between
alpha=alpha)
File "path/lib/python3.7/site-packages/matplotlib/init.py", line 1601, in inner
return func(ax, *map(sanitize_sequence, args), **kwargs)
File "path/lib/python3.7/site-packages/matplotlib/axes/_axes.py", line 5236, in fill_between
map(np.ma.getmask, [x, y1, y2]))
TypeError: ufunc 'bitwise_and' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

runx1.bed content is below:

chr21 34881498 34893033 Promoter
chr21 34801639 34805234 E4
chr21 34807659 34812355 E5
chr21 34842207 34848567 E6
chr21 34864184 34869181 E7
chr21 34908356 34913168 E8
chr21 34926640 34939079 E9
chr21 34940554 34954420 E10
chr21 34967539 34976280 E11
chr21 34983047 34991725 E12
chr21 34995173 35000524 E13

chr21.ixy is produced by :
cLoops2 pre -f ./K562_HiTrac_bio2.bedpe.gz -o k562_bio2 -c chr21

Best Wishes,
poflawless

Hello Dr/Pro Gao,

When I tryied to use the command as below to call domain, cloops2 raised an error: IndexError: tuple index out of range
cLoops2 callDomains -d Pre_sample1_merge_sampled -o Pre_sample1_merge_sampled_Domain -bs 1000,5000 -ws 500,1000,5000 -p 12,

what can I do to correct it?

Thanks a lot for your help

Hi Yaqiang,

I'm trying to call loops for Micro-C data by this command, and it shows error.

`
#SBATCH -o log.cLoops2.05.call-loops-%j.o
#SBATCH -e log.cLoops2.05.call-loops-%j.e
#SBATCH -N 2
#SBATCH -n 3
#SBATCH -c 10
#SBATCH --mem-per-cpu=20G
#SBATCH -t 3-1

path='.'

folder_list=$(find ${path}/*.cLoops2 -type d)

for folder_name in ${folder_list}; do

echo "=== sample: ${folder_name} ==="
echo -e "\n\t call loops for ${folder_name} at $(date +%Y"-"%m"-"%d" "%H":"%M":"%S) \n"

cLoops2 callLoops -d ${folder_name} -o ${folder_name} -eps 1500,2500,5000,10000 -minPts 25,50,100 -cut 1000 -p 50 -w -j -i -hic -trans

done
`

It shows error:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/wangs16/anaconda3/envs/cLoops2-3.10/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/wangs16/.local/lib/python3.10/site-packages/joblib/_parallel_backends.py", line 620, in call
return self.func(*args, **kwargs)
File "/home/wangs16/.local/lib/python3.10/site-packages/joblib/parallel.py", line 288, in call
return [func(*args, **kwargs)
File "/home/wangs16/.local/lib/python3.10/site-packages/joblib/parallel.py", line 288, in
return [func(*args, **kwargs)
File "/home/wangs16/.local/lib/python3.10/site-packages/cLoops2/callCisLoops.py", line 78, in runCisDBSCANLoops
report = "No PETs found in %s, maybe due to cut > %" % (fixy, cut)
ValueError: incomplete format
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/wangs16/anaconda3/envs/cLoops2-3.10/bin/cLoops2", line 33, in
sys.exit(load_entry_point('cLoops2==0.0.5', 'console_scripts', 'cLoops2')())
File "/home/wangs16/.local/lib/python3.10/site-packages/cLoops2/cLoops2.py", line 3679, in main
callCisLoops(
File "/home/wangs16/.local/lib/python3.10/site-packages/cLoops2/callCisLoops.py", line 557, in callCisLoops
loops_2, dis_2, dss_2 = parallelRunCisDBSCANLoops(
File "/home/wangs16/.local/lib/python3.10/site-packages/cLoops2/callCisLoops.py", line 139, in parallelRunCisDBSCANLoops
ds = Parallel(n_jobs=cpu,backend="multiprocessing")(delayed(runCisDBSCANLoops)(
File "/home/wangs16/.local/lib/python3.10/site-packages/joblib/parallel.py", line 1098, in call
self.retrieve()
File "/home/wangs16/.local/lib/python3.10/site-packages/joblib/parallel.py", line 975, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/home/wangs16/anaconda3/envs/cLoops2-3.10/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: incomplete format

2023-06-22 15:55:00 cLoops2 INFO Command: cLoops2 callLoops -d ./01.cLoops2 -eps 1500,2500,5000,10000 -minPts 25,50,100 -p 20 -o ./01.cLoops2 -cut 1000 -mcut -1 -filter False -i True -j True -w True -hic True -max_cut False -trans True -emPair False
2023-06-22 15:55:00 cLoops2 INFO -hic option selected, cDBSCAN2 is used instead of blockDBSCAN.
2023-06-22 15:55:00 cLoops2 INFO Clustering chrM and chrM using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chrY and chrY using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chrY_random and chrY_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chrY_random and chrY_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chr8_random and chr8_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chr4_random and chr4_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chr4_random and chr4_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chr1_random and chr1_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chrX_random and chrX_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chr13_random and chr13_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chr13_random and chr13_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chrM and chrM finished. Estimated 219 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chr8_random and chr8_random finished. Estimated 260 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chrX_random and chrX_random finished. Estimated 682 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:00 cLoops2 INFO Clustering chrUn_random and chrUn_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chr9_random and chr9_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:00 cLoops2 INFO Clustering chr9_random and chr9_random finished. Estimated 106 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:55:01 cLoops2 INFO Clustering chrUn_random and chrUn_random finished. Estimated 884 self-ligation reads and 2386 inter-ligation reads, 6 candidate loops.
2023-06-22 15:55:02 cLoops2 INFO Clustering chr1_random and chr1_random finished. Estimated 12665 self-ligation reads and 316 inter-ligation reads, 2 candidate loops.
2023-06-22 15:55:03 cLoops2 INFO Clustering chrX and chrX using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:04 cLoops2 INFO Clustering chr17 and chr17 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:04 cLoops2 INFO Clustering chr19 and chr19 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:04 cLoops2 INFO Clustering chr18 and chr18 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:05 cLoops2 INFO Clustering chr15 and chr15 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:05 cLoops2 INFO Clustering chr16 and chr16 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:06 cLoops2 INFO Clustering chr13 and chr13 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:07 cLoops2 INFO Clustering chr6 and chr6 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:07 cLoops2 INFO Clustering chr9 and chr9 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:07 cLoops2 INFO Clustering chr10 and chr10 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:07 cLoops2 INFO Clustering chr12 and chr12 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:07 cLoops2 INFO Clustering chr8 and chr8 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:08 cLoops2 INFO Clustering chr11 and chr11 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:08 cLoops2 INFO Clustering chr14 and chr14 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:09 cLoops2 INFO Clustering chr7 and chr7 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:10 cLoops2 INFO Clustering chr2 and chr2 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:10 cLoops2 INFO Clustering chr4 and chr4 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:10 cLoops2 INFO Clustering chr3 and chr3 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:16 cLoops2 INFO Clustering chr5 and chr5 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:55:22 cLoops2 INFO Clustering chr1 and chr1 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 15:56:19 cLoops2 INFO Clustering chrX and chrX finished. Estimated 7510 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 15:59:09 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 665473 self-ligation reads and 2359 inter-ligation reads, 17 candidate loops.
2023-06-22 15:59:20 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 444533 self-ligation reads and 4230 inter-ligation reads, 24 candidate loops.
2023-06-22 16:00:18 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 299563 self-ligation reads and 1839 inter-ligation reads, 13 candidate loops.
2023-06-22 16:00:20 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 487105 self-ligation reads and 1876 inter-ligation reads, 14 candidate loops.
2023-06-22 16:00:45 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 833519 self-ligation reads and 6505 inter-ligation reads, 28 candidate loops.
2023-06-22 16:00:53 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 805234 self-ligation reads and 2749 inter-ligation reads, 20 candidate loops.
2023-06-22 16:01:02 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 711989 self-ligation reads and 3074 inter-ligation reads, 22 candidate loops.
2023-06-22 16:01:06 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 449155 self-ligation reads and 2660 inter-ligation reads, 21 candidate loops.
2023-06-22 16:01:58 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 816028 self-ligation reads and 4300 inter-ligation reads, 33 candidate loops.
2023-06-22 16:02:52 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 844997 self-ligation reads and 13792 inter-ligation reads, 33 candidate loops.
2023-06-22 16:02:55 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 1192327 self-ligation reads and 5841 inter-ligation reads, 35 candidate loops.
2023-06-22 16:03:03 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 1441314 self-ligation reads and 9706 inter-ligation reads, 60 candidate loops.
2023-06-22 16:03:22 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 907053 self-ligation reads and 2549 inter-ligation reads, 17 candidate loops.
2023-06-22 16:04:52 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 1420743 self-ligation reads and 5446 inter-ligation reads, 40 candidate loops.
2023-06-22 16:05:32 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 1725449 self-ligation reads and 7087 inter-ligation reads, 35 candidate loops.
2023-06-22 16:05:40 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 1572304 self-ligation reads and 7872 inter-ligation reads, 50 candidate loops.
2023-06-22 16:06:17 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 1422445 self-ligation reads and 7056 inter-ligation reads, 47 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Command: cLoops2 callLoops -d ./02.cLoops2 -eps 1500,2500,5000,10000 -minPts 25,50,100 -p 20 -o ./02.cLoops2 -cut 1000 -mcut -1 -filter False -i True -j True -w True -hic True -max_cut False -trans True -emPair False
2023-06-22 16:06:25 cLoops2 INFO -hic option selected, cDBSCAN2 is used instead of blockDBSCAN.
2023-06-22 16:06:25 cLoops2 INFO Clustering chrM and chrM using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chrY and chrY using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chrY_random and chrY_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chrY_random and chrY_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chr8_random and chr8_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chr4_random and chr4_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chr4_random and chr4_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chrX_random and chrX_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chrM and chrM finished. Estimated 152 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chr13_random and chr13_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chr13_random and chr13_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chr1_random and chr1_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chr8_random and chr8_random finished. Estimated 281 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chrUn_random and chrUn_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chrX_random and chrX_random finished. Estimated 643 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:25 cLoops2 INFO Clustering chr9_random and chr9_random using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:25 cLoops2 INFO Clustering chr9_random and chr9_random finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:26 cLoops2 INFO Clustering chr17 and chr17 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:26 cLoops2 INFO Clustering chr19 and chr19 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:26 cLoops2 INFO Clustering chr1_random and chr1_random finished. Estimated 8620 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-22 16:06:26 cLoops2 INFO Clustering chr15 and chr15 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:26 cLoops2 INFO Clustering chrX and chrX using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:27 cLoops2 INFO Clustering chrUn_random and chrUn_random finished. Estimated 1406 self-ligation reads and 4309 inter-ligation reads, 13 candidate loops.
2023-06-22 16:06:27 cLoops2 INFO Clustering chr11 and chr11 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:27 cLoops2 INFO Clustering chr12 and chr12 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:27 cLoops2 INFO Clustering chr13 and chr13 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:28 cLoops2 INFO Clustering chr14 and chr14 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:28 cLoops2 INFO Clustering chr10 and chr10 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:28 cLoops2 INFO Clustering chr16 and chr16 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:28 cLoops2 INFO Clustering chr18 and chr18 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:28 cLoops2 INFO Clustering chr7 and chr7 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:29 cLoops2 INFO Clustering chr4 and chr4 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:29 cLoops2 INFO Clustering chr9 and chr9 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:29 cLoops2 INFO Clustering chr2 and chr2 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:30 cLoops2 INFO Clustering chr8 and chr8 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:30 cLoops2 INFO Clustering chr3 and chr3 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:30 cLoops2 INFO Clustering chr5 and chr5 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:31 cLoops2 INFO Clustering chr6 and chr6 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:06:34 cLoops2 INFO Clustering chr1 and chr1 using eps 1500, minPts 100,pre-set distance cutoff > 1000
2023-06-22 16:07:39 cLoops2 INFO Clustering chrX and chrX finished. Estimated 8207 self-ligation reads and 137 inter-ligation reads, 1 candidate loops.
2023-06-22 16:08:29 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 318564 self-ligation reads and 1291 inter-ligation reads, 10 candidate loops.
2023-06-22 16:09:53 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 98242 self-ligation reads and 1050 inter-ligation reads, 8 candidate loops.
2023-06-22 16:10:00 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 209309 self-ligation reads and 3342 inter-ligation reads, 19 candidate loops.
2023-06-22 16:10:08 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 195235 self-ligation reads and 582 inter-ligation reads, 4 candidate loops.
2023-06-22 16:10:08 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 267042 self-ligation reads and 1697 inter-ligation reads, 12 candidate loops.
2023-06-22 16:10:14 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 344915 self-ligation reads and 3910 inter-ligation reads, 20 candidate loops.
2023-06-22 16:10:35 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 425822 self-ligation reads and 1916 inter-ligation reads, 16 candidate loops.
2023-06-22 16:11:19 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 218821 self-ligation reads and 2170 inter-ligation reads, 17 candidate loops.
2023-06-22 16:11:26 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 488097 self-ligation reads and 3135 inter-ligation reads, 22 candidate loops.
2023-06-22 16:11:31 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 284235 self-ligation reads and 15998 inter-ligation reads, 22 candidate loops.
2023-06-22 16:12:00 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 372326 self-ligation reads and 1626 inter-ligation reads, 13 candidate loops.
2023-06-22 16:12:07 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 604331 self-ligation reads and 4153 inter-ligation reads, 26 candidate loops.
2023-06-22 16:12:29 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 923207 self-ligation reads and 7032 inter-ligation reads, 42 candidate loops.
2023-06-22 16:12:57 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 591732 self-ligation reads and 3754 inter-ligation reads, 28 candidate loops.
2023-06-22 16:13:11 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 766333 self-ligation reads and 5431 inter-ligation reads, 30 candidate loops.
2023-06-22 16:13:46 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 776084 self-ligation reads and 6013 inter-ligation reads, 44 candidate loops.
2023-06-22 16:14:06 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 528096 self-ligation reads and 4503 inter-ligation reads, 25 candidate loops.

Thank you!

Best,
Charles

Hi author:
I want to know how convert the matrix file produced by HiC-Pro to the cloops data.
Nutures

Hello,

I am trying to plot loops in a bedpe file.

I understand I should use the function plot.plotLoops

However, can you please give me an example on the parameter loops in the function. Is it a dataframe? Can you please point me to an example using this function with its available data?

Thanks