Error in cLoops2 callLoops about cloops2

[CW20221031]

I tried both -p 50 and -p 20, but neither works.

[YaqiangCao]

I would like to suggest remove chromosomes like chrUn_random and chrUn_random with cLoops2 pre -cs, input only "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, chrX".

[CW20221031]

Hi Yaqiang,

Thank you for your reply! I used "cLoops2 pre -cs" to regenerate cLoops2 data files from bedpe files. But why there's no .ixy files produced in the cLoops2 folder, but only one "petMeta.json" file, with the content:
{"Total PETs": 0, "High Mapq(>=0) PETs": 0, "Total Trans PETs": 0, "Total Cis PETs": 0, "Filtered too close (<0) PETs": 0, "Filtered too distant (>-1) PETs": 0, "Unique PETs": 0, "Cis PETs Redundancy": 0, "data": {"cis": {}, "trans": {}}}

---

The content of cLoops2.log file:

2023-06-25 03:08:41 cLoops2 INFO Command: cLoops2 pre -f ./01.bedpe -o 01.cLoops2.2 -p 50 -c s -cut 0 -mcut -1 -mapq 0 -trans False -format bedpe
2023-06-25 03:08:41 cLoops2 INFO Parsing PETs from ./01.bedpe, requiring initial distance cutoff >0 and <-1
2023-06-25 03:30:06 cLoops2 INFO Totaly 0 PETs in target chromosomes from ./01.bedpe, in which 0 high quality unqiue PETs
2023-06-25 03:30:06 cLoops2 INFO writing .ixy files
2023-06-25 03:30:06 cLoops2 INFO cLoops2 pre finished. Used time: 0:21:24.566764.

---

In addition, can I simply delete the .ixy files with chromosomes like chrUn_random and chrUn_random in the cLoops2 data folders that I generated previously? Do I need to update the folder after deleting these files with "cLoops2 update" or any other commands?

Thanks!

Best,
Charles

[YaqiangCao]

Hi Yaqiang,

Thank you for your reply! I used "cLoops2 pre -cs" to regenerate cLoops2 data files from bedpe files. But why there's no .ixy files produced in the cLoops2 folder, but only one "petMeta.json" file, with the content: {"Total PETs": 0, "High Mapq(>=0) PETs": 0, "Total Trans PETs": 0, "Total Cis PETs": 0, "Filtered too close (<0) PETs": 0, "Filtered too distant (>-1) PETs": 0, "Unique PETs": 0, "Cis PETs Redundancy": 0, "data": {"cis": {}, "trans": {}}}

The content of cLoops2.log file:

2023-06-25 03:08:41 cLoops2 INFO Command: cLoops2 pre -f ./01.bedpe -o 01.cLoops2.2 -p 50 -c s -cut 0 -mcut -1 -mapq 0 -trans False -format bedpe 2023-06-25 03:08:41 cLoops2 INFO Parsing PETs from ./01.bedpe, requiring initial distance cutoff >0 and <-1 2023-06-25 03:30:06 cLoops2 INFO Totaly 0 PETs in target chromosomes from ./01.bedpe, in which 0 high quality unqiue PETs 2023-06-25 03:30:06 cLoops2 INFO writing .ixy files 2023-06-25 03:30:06 cLoops2 INFO cLoops2 pre finished. Used time: 0:21:24.566764.

In addition, can I simply delete the .ixy files with chromosomes like chrUn_random and chrUn_random in the cLoops2 data folders that I generated previously? Do I need to update the folder after deleting these files with "cLoops2 update" or any other commands?

Thanks!

Best, Charles

It can be used as cLoops2 pre -c "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, chrX" . -c s does not have any meaning. My fault with previous email for fuzzy explanation.

You can delete the .ixy files you do not want and then run cLoops2 update to update the .json file for downstream analysis.

Good luck.

[CW20221031]

I tried to call loops after deleting the .ixy files with chromosomes like chrUn_random and chrUn_random in the cLoops2 data folders and then updated the .json file by cLoops2 update. But the error message is the same and no loop files were generated.

The error message is:

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 34, 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

The cLoops2.log is:

2023-06-25 16:42:37 cLoops2 INFO Command: cLoops2 callLoops -d ./01.cLoops2.2 -eps 2500,5000,10000 -minPts 25,50,100 -p 50 -o ./01.cLoops2.2 -cut 1000 -mcut -1 -filter False -i True -j True -w True -hic True -max_cut False -trans False -emPair False
2023-06-25 16:42:37 cLoops2 INFO -hic option selected, cDBSCAN2 is used instead of blockDBSCAN.
2023-06-25 16:42:38 cLoops2 INFO Clustering chrM and chrM using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:38 cLoops2 INFO Clustering chrY and chrY using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:38 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 16:42:38 cLoops2 INFO Clustering chrM and chrM finished. Estimated 386 self-ligation reads and 503 inter-ligation reads, 1 candidate loops.
2023-06-25 16:42:39 cLoops2 INFO Clustering chrX and chrX using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:39 cLoops2 INFO Clustering chr10 and chr10 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:39 cLoops2 INFO Clustering chr19 and chr19 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr18 and chr18 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr16 and chr16 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr17 and chr17 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr15 and chr15 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr12 and chr12 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr13 and chr13 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr11 and chr11 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr14 and chr14 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr6 and chr6 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr5 and chr5 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr3 and chr3 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr9 and chr9 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr2 and chr2 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:42 cLoops2 INFO Clustering chr4 and chr4 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:42 cLoops2 INFO Clustering chr7 and chr7 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:42 cLoops2 INFO Clustering chr8 and chr8 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:45 cLoops2 INFO Clustering chr1 and chr1 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:44:09 cLoops2 INFO Clustering chrX and chrX finished. Estimated 104503 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 16:49:08 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 2111177 self-ligation reads and 4561 inter-ligation reads, 28 candidate loops.
2023-06-25 16:50:23 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 2240217 self-ligation reads and 7719 inter-ligation reads, 45 candidate loops.
2023-06-25 16:50:54 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 2506965 self-ligation reads and 10640 inter-ligation reads, 47 candidate loops.
2023-06-25 16:51:02 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 2428547 self-ligation reads and 5898 inter-ligation reads, 39 candidate loops.
2023-06-25 16:51:42 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 2530786 self-ligation reads and 6593 inter-ligation reads, 38 candidate loops.
2023-06-25 16:52:19 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 2337032 self-ligation reads and 4623 inter-ligation reads, 30 candidate loops.
2023-06-25 16:53:03 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 2579736 self-ligation reads and 6752 inter-ligation reads, 44 candidate loops.
2023-06-25 16:53:46 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 3079319 self-ligation reads and 8669 inter-ligation reads, 58 candidate loops.
2023-06-25 16:53:57 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 2773870 self-ligation reads and 5556 inter-ligation reads, 38 candidate loops.
2023-06-25 16:54:37 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 3605355 self-ligation reads and 19631 inter-ligation reads, 98 candidate loops.
2023-06-25 16:55:49 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 3639109 self-ligation reads and 17682 inter-ligation reads, 54 candidate loops.
2023-06-25 16:55:51 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 3523667 self-ligation reads and 13122 inter-ligation reads, 77 candidate loops.
2023-06-25 16:56:19 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 3518936 self-ligation reads and 5822 inter-ligation reads, 37 candidate loops.
2023-06-25 16:57:08 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 4912785 self-ligation reads and 11592 inter-ligation reads, 52 candidate loops.
2023-06-25 16:57:09 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 4339006 self-ligation reads and 11463 inter-ligation reads, 69 candidate loops.
2023-06-25 16:57:58 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 4463507 self-ligation reads and 14674 inter-ligation reads, 84 candidate loops.
2023-06-25 16:58:04 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 4889701 self-ligation reads and 17885 inter-ligation reads, 93 candidate loops.
2023-06-25 17:00:27 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 5011907 self-ligation reads and 12476 inter-ligation reads, 71 candidate loops.
2023-06-25 17:06:04 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 7872768 self-ligation reads and 34178 inter-ligation reads, 172 candidate loops.
2023-06-25 17:06:18 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 9824 for eps=2500,minPts=100
2023-06-25 17:06:20 cLoops2 INFO Clustering chrM and chrM using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:20 cLoops2 INFO Clustering chrY and chrY using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:20 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:06:20 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 277 inter-ligation reads, 1 candidate loops.
2023-06-25 17:06:21 cLoops2 INFO Clustering chr17 and chr17 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chrX and chrX using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chr19 and chr19 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chr18 and chr18 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chr16 and chr16 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr2 and chr2 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr15 and chr15 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr13 and chr13 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr14 and chr14 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr3 and chr3 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr12 and chr12 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr8 and chr8 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr10 and chr10 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr11 and chr11 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr9 and chr9 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr5 and chr5 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr4 and chr4 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr7 and chr7 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr6 and chr6 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:26 cLoops2 INFO Clustering chr1 and chr1 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:07:16 cLoops2 INFO Clustering chrX and chrX finished. Estimated 0 self-ligation reads and 1950 inter-ligation reads, 4 candidate loops.
2023-06-25 17:07:35 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 0 self-ligation reads and 6283 inter-ligation reads, 53 candidate loops.
2023-06-25 17:07:52 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 0 self-ligation reads and 11811 inter-ligation reads, 84 candidate loops.
2023-06-25 17:07:55 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 0 self-ligation reads and 5915 inter-ligation reads, 43 candidate loops.
2023-06-25 17:07:57 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 0 self-ligation reads and 3631 inter-ligation reads, 36 candidate loops.
2023-06-25 17:07:59 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 0 self-ligation reads and 7011 inter-ligation reads, 53 candidate loops.
2023-06-25 17:08:05 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 0 self-ligation reads and 3973 inter-ligation reads, 43 candidate loops.
2023-06-25 17:08:07 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 0 self-ligation reads and 7700 inter-ligation reads, 55 candidate loops.
2023-06-25 17:08:12 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 0 self-ligation reads and 9846 inter-ligation reads, 102 candidate loops.
2023-06-25 17:08:17 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 864 self-ligation reads and 15100 inter-ligation reads, 64 candidate loops.
2023-06-25 17:08:18 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 0 self-ligation reads and 6909 inter-ligation reads, 61 candidate loops.
2023-06-25 17:08:20 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 0 self-ligation reads and 30128 inter-ligation reads, 201 candidate loops.
2023-06-25 17:08:26 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 0 self-ligation reads and 5139 inter-ligation reads, 49 candidate loops.
2023-06-25 17:08:27 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 1062 self-ligation reads and 16496 inter-ligation reads, 138 candidate loops.
2023-06-25 17:08:29 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 380 self-ligation reads and 20780 inter-ligation reads, 167 candidate loops.
2023-06-25 17:08:35 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 0 self-ligation reads and 12440 inter-ligation reads, 107 candidate loops.
2023-06-25 17:08:35 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 28739 self-ligation reads and 19853 inter-ligation reads, 152 candidate loops.
2023-06-25 17:08:40 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 910 self-ligation reads and 19578 inter-ligation reads, 166 candidate loops.
2023-06-25 17:08:44 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 0 self-ligation reads and 13187 inter-ligation reads, 108 candidate loops.
2023-06-25 17:09:38 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 919 self-ligation reads and 43564 inter-ligation reads, 320 candidate loops.
2023-06-25 17:09:41 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 7938 for eps=2500,minPts=50
2023-06-25 17:09:41 cLoops2 INFO Clustering chrM and chrM using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:41 cLoops2 INFO Clustering chrY and chrY using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:41 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:09:41 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 411 inter-ligation reads, 1 candidate loops.
2023-06-25 17:09:42 cLoops2 INFO Clustering chr16 and chr16 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chr19 and chr19 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chrX and chrX using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chr18 and chr18 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chr15 and chr15 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr10 and chr10 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr13 and chr13 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr2 and chr2 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr6 and chr6 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr9 and chr9 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr8 and chr8 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr17 and chr17 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr1 and chr1 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr4 and chr4 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr11 and chr11 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr14 and chr14 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr5 and chr5 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr12 and chr12 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:44 cLoops2 INFO Clustering chr3 and chr3 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:44 cLoops2 INFO Clustering chr7 and chr7 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:10:26 cLoops2 INFO Clustering chrX and chrX finished. Estimated 2485 self-ligation reads and 2571 inter-ligation reads, 58 candidate loops.
2023-06-25 17:11:20 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 47906 self-ligation reads and 92013 inter-ligation reads, 1621 candidate loops.
2023-06-25 17:11:31 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 18005 self-ligation reads and 73569 inter-ligation reads, 1359 candidate loops.
2023-06-25 17:11:48 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 62753 self-ligation reads and 122493 inter-ligation reads, 2017 candidate loops.
2023-06-25 17:11:52 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 47580 self-ligation reads and 100371 inter-ligation reads, 1825 candidate loops.
2023-06-25 17:11:52 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 40487 self-ligation reads and 77739 inter-ligation reads, 1417 candidate loops.
2023-06-25 17:11:55 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 5986 self-ligation reads and 64437 inter-ligation reads, 1341 candidate loops.
2023-06-25 17:12:23 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 41121 self-ligation reads and 110178 inter-ligation reads, 1902 candidate loops.
2023-06-25 17:12:38 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 29873 self-ligation reads and 77886 inter-ligation reads, 1454 candidate loops.
2023-06-25 17:12:44 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 57808 self-ligation reads and 102883 inter-ligation reads, 1868 candidate loops.
2023-06-25 17:13:11 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 127940 self-ligation reads and 156111 inter-ligation reads, 2557 candidate loops.
2023-06-25 17:13:12 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 38895 self-ligation reads and 142632 inter-ligation reads, 2509 candidate loops.
2023-06-25 17:13:15 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 37326 self-ligation reads and 125331 inter-ligation reads, 2442 candidate loops.
2023-06-25 17:13:16 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 123767 self-ligation reads and 141381 inter-ligation reads, 2407 candidate loops.
2023-06-25 17:13:59 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 86652 self-ligation reads and 199175 inter-ligation reads, 3396 candidate loops.
2023-06-25 17:14:12 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 163026 self-ligation reads and 230874 inter-ligation reads, 3893 candidate loops.
2023-06-25 17:14:18 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 89766 self-ligation reads and 207738 inter-ligation reads, 3563 candidate loops.
2023-06-25 17:14:34 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 145548 self-ligation reads and 229686 inter-ligation reads, 3891 candidate loops.
2023-06-25 17:14:40 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 75598 self-ligation reads and 211767 inter-ligation reads, 3807 candidate loops.
2023-06-25 17:17:35 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 309812 self-ligation reads and 360314 inter-ligation reads, 5879 candidate loops.
2023-06-25 17:17:38 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 7143 for eps=2500,minPts=25
2023-06-25 17:17:39 cLoops2 INFO Clustering chrY and chrY using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:39 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:17:39 cLoops2 INFO Clustering chrM and chrM using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:39 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 448 inter-ligation reads, 1 candidate loops.
2023-06-25 17:17:39 cLoops2 INFO Clustering chr18 and chr18 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:39 cLoops2 INFO Clustering chrX and chrX using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr14 and chr14 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr8 and chr8 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr4 and chr4 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr17 and chr17 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr15 and chr15 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr19 and chr19 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr13 and chr13 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr10 and chr10 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr9 and chr9 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr6 and chr6 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr7 and chr7 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr3 and chr3 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr5 and chr5 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr16 and chr16 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr12 and chr12 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr11 and chr11 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:44 cLoops2 INFO Clustering chr2 and chr2 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:44 cLoops2 INFO Clustering chr1 and chr1 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:18:23 cLoops2 INFO Clustering chrX and chrX finished. Estimated 2928 self-ligation reads and 463 inter-ligation reads, 3 candidate loops.
2023-06-25 17:18:54 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 64378 self-ligation reads and 31924 inter-ligation reads, 195 candidate loops.
2023-06-25 17:19:07 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 27245 self-ligation reads and 24414 inter-ligation reads, 152 candidate loops.
2023-06-25 17:19:18 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 8263 self-ligation reads and 17617 inter-ligation reads, 112 candidate loops.
2023-06-25 17:19:20 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 84460 self-ligation reads and 47459 inter-ligation reads, 272 candidate loops.
2023-06-25 17:19:21 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 65070 self-ligation reads and 29851 inter-ligation reads, 193 candidate loops.
2023-06-25 17:19:24 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 56852 self-ligation reads and 40457 inter-ligation reads, 251 candidate loops.
2023-06-25 17:19:26 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 56136 self-ligation reads and 24836 inter-ligation reads, 154 candidate loops.
2023-06-25 17:19:29 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 77574 self-ligation reads and 35350 inter-ligation reads, 227 candidate loops.
2023-06-25 17:19:31 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 39652 self-ligation reads and 24940 inter-ligation reads, 152 candidate loops.
2023-06-25 17:19:40 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 55836 self-ligation reads and 47060 inter-ligation reads, 264 candidate loops.
2023-06-25 17:19:44 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 49750 self-ligation reads and 31799 inter-ligation reads, 223 candidate loops.
2023-06-25 17:19:52 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 157716 self-ligation reads and 51655 inter-ligation reads, 298 candidate loops.
2023-06-25 17:19:54 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 168552 self-ligation reads and 65937 inter-ligation reads, 354 candidate loops.
2023-06-25 17:20:12 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 120714 self-ligation reads and 71633 inter-ligation reads, 461 candidate loops.
2023-06-25 17:20:14 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 211831 self-ligation reads and 86278 inter-ligation reads, 512 candidate loops.
2023-06-25 17:20:25 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 130276 self-ligation reads and 72665 inter-ligation reads, 477 candidate loops.
2023-06-25 17:20:30 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 197924 self-ligation reads and 84823 inter-ligation reads, 501 candidate loops.
2023-06-25 17:20:35 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 105113 self-ligation reads and 68633 inter-ligation reads, 425 candidate loops.
2023-06-25 17:22:09 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 417345 self-ligation reads and 138165 inter-ligation reads, 783 candidate loops.
2023-06-25 17:22:12 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 6298 for eps=5000,minPts=100
2023-06-25 17:22:13 cLoops2 INFO Clustering chrY and chrY using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:13 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:22:13 cLoops2 INFO Clustering chrM and chrM using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:13 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 475 inter-ligation reads, 1 candidate loops.
2023-06-25 17:22:14 cLoops2 INFO Clustering chr15 and chr15 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chrX and chrX using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr18 and chr18 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr17 and chr17 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr16 and chr16 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr4 and chr4 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr19 and chr19 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr10 and chr10 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr13 and chr13 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr14 and chr14 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr3 and chr3 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr9 and chr9 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr8 and chr8 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr6 and chr6 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr7 and chr7 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr12 and chr12 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr5 and chr5 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr11 and chr11 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:16 cLoops2 INFO Clustering chr2 and chr2 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:17 cLoops2 INFO Clustering chr1 and chr1 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:23:05 cLoops2 INFO Clustering chrX and chrX finished. Estimated 16653 self-ligation reads and 7951 inter-ligation reads, 112 candidate loops.
2023-06-25 17:24:17 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 504305 self-ligation reads and 58623 inter-ligation reads, 599 candidate loops.
2023-06-25 17:24:54 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 592410 self-ligation reads and 77901 inter-ligation reads, 743 candidate loops.
2023-06-25 17:25:00 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 427355 self-ligation reads and 73505 inter-ligation reads, 845 candidate loops.
2023-06-25 17:25:20 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 545938 self-ligation reads and 62948 inter-ligation reads, 655 candidate loops.
2023-06-25 17:25:21 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 551508 self-ligation reads and 80876 inter-ligation reads, 853 candidate loops.
2023-06-25 17:25:44 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 480534 self-ligation reads and 74481 inter-ligation reads, 867 candidate loops.
2023-06-25 17:26:12 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 611982 self-ligation reads and 98902 inter-ligation reads, 1035 candidate loops.
2023-06-25 17:26:19 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 463886 self-ligation reads and 92361 inter-ligation reads, 1181 candidate loops.
2023-06-25 17:26:19 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 481358 self-ligation reads and 90829 inter-ligation reads, 1060 candidate loops.
2023-06-25 17:26:31 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 831678 self-ligation reads and 116667 inter-ligation reads, 1027 candidate loops.
2023-06-25 17:26:46 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 739789 self-ligation reads and 88473 inter-ligation reads, 1019 candidate loops.
2023-06-25 17:26:48 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 806691 self-ligation reads and 109282 inter-ligation reads, 1105 candidate loops.
2023-06-25 17:26:57 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 776988 self-ligation reads and 109470 inter-ligation reads, 1139 candidate loops.
2023-06-25 17:27:00 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 1235231 self-ligation reads and 141234 inter-ligation reads, 1227 candidate loops.
2023-06-25 17:27:09 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 986027 self-ligation reads and 126541 inter-ligation reads, 1242 candidate loops.
2023-06-25 17:27:29 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 1006039 self-ligation reads and 126547 inter-ligation reads, 1258 candidate loops.
2023-06-25 17:27:42 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 1157184 self-ligation reads and 139360 inter-ligation reads, 1252 candidate loops.
2023-06-25 17:28:21 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 1124564 self-ligation reads and 146249 inter-ligation reads, 1500 candidate loops.
2023-06-25 17:30:24 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 1867887 self-ligation reads and 212919 inter-ligation reads, 1817 candidate loops.
2023-06-25 17:30:30 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 5162 for eps=5000,minPts=50
2023-06-25 17:30:31 cLoops2 INFO Clustering chrY and chrY using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:31 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:30:31 cLoops2 INFO Clustering chrM and chrM using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:31 cLoops2 INFO Clustering chrM and chrM finished. Estimated 498 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:30:32 cLoops2 INFO Clustering chrX and chrX using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr12 and chr12 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr19 and chr19 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr6 and chr6 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr18 and chr18 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr17 and chr17 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr15 and chr15 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr13 and chr13 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr14 and chr14 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr3 and chr3 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr16 and chr16 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr11 and chr11 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr7 and chr7 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr10 and chr10 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr4 and chr4 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr9 and chr9 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr8 and chr8 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:35 cLoops2 INFO Clustering chr5 and chr5 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:35 cLoops2 INFO Clustering chr1 and chr1 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:35 cLoops2 INFO Clustering chr2 and chr2 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:32:12 cLoops2 INFO Clustering chrX and chrX finished. Estimated 225876 self-ligation reads and 35518 inter-ligation reads, 994 candidate loops.
2023-06-25 17:33:18 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 1019542 self-ligation reads and 79609 inter-ligation reads, 1095 candidate loops.
2023-06-25 17:34:10 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 1047853 self-ligation reads and 95191 inter-ligation reads, 1392 candidate loops.
2023-06-25 17:34:23 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 1214445 self-ligation reads and 120818 inter-ligation reads, 1604 candidate loops.
2023-06-25 17:34:41 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 1179767 self-ligation reads and 108230 inter-ligation reads, 1565 candidate loops.
2023-06-25 17:34:44 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 1258567 self-ligation reads and 115264 inter-ligation reads, 1623 candidate loops.
2023-06-25 17:35:00 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 1277419 self-ligation reads and 96596 inter-ligation reads, 1505 candidate loops.
2023-06-25 17:35:14 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 1257134 self-ligation reads and 99499 inter-ligation reads, 1681 candidate loops.
2023-06-25 17:35:33 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 1438140 self-ligation reads and 125750 inter-ligation reads, 1792 candidate loops.
2023-06-25 17:36:02 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 1705257 self-ligation reads and 153035 inter-ligation reads, 2147 candidate loops.
2023-06-25 17:36:03 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 1676018 self-ligation reads and 171429 inter-ligation reads, 2140 candidate loops.
2023-06-25 17:36:09 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 1724178 self-ligation reads and 144374 inter-ligation reads, 1894 candidate loops.
2023-06-25 17:36:24 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 1677707 self-ligation reads and 138430 inter-ligation reads, 2295 candidate loops.
2023-06-25 17:36:38 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 1337696 self-ligation reads and 131550 inter-ligation reads, 2186 candidate loops.
2023-06-25 17:36:39 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 2333323 self-ligation reads and 186306 inter-ligation reads, 2173 candidate loops.
2023-06-25 17:36:44 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 1989989 self-ligation reads and 185087 inter-ligation reads, 2505 candidate loops.
2023-06-25 17:37:25 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 2101063 self-ligation reads and 187947 inter-ligation reads, 2552 candidate loops.
2023-06-25 17:37:58 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 2421585 self-ligation reads and 200858 inter-ligation reads, 2807 candidate loops.
2023-06-25 17:37:59 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 2254391 self-ligation reads and 217258 inter-ligation reads, 2894 candidate loops.
2023-06-25 17:41:35 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 3483648 self-ligation reads and 351894 inter-ligation reads, 4188 candidate loops.
2023-06-25 17:41:43 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 2586 for eps=5000,minPts=25
2023-06-25 17:41:44 cLoops2 INFO Clustering chrY and chrY using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:44 cLoops2 INFO Clustering chrM and chrM using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:44 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:41:44 cLoops2 INFO Clustering chrM and chrM finished. Estimated 635 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:41:45 cLoops2 INFO Clustering chr19 and chr19 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:45 cLoops2 INFO Clustering chrX and chrX using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:45 cLoops2 INFO Clustering chr14 and chr14 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:45 cLoops2 INFO Clustering chr12 and chr12 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr18 and chr18 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr17 and chr17 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr13 and chr13 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr3 and chr3 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr16 and chr16 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr9 and chr9 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr15 and chr15 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr6 and chr6 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr10 and chr10 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr7 and chr7 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr11 and chr11 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr5 and chr5 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr8 and chr8 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:48 cLoops2 INFO Clustering chr4 and chr4 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:49 cLoops2 INFO Clustering chr1 and chr1 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:49 cLoops2 INFO Clustering chr2 and chr2 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:43:56 cLoops2 INFO Clustering chrX and chrX finished. Estimated 627752 self-ligation reads and 3499 inter-ligation reads, 17 candidate loops.
2023-06-25 17:47:22 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 1871918 self-ligation reads and 27254 inter-ligation reads, 100 candidate loops.
2023-06-25 17:47:55 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 2112366 self-ligation reads and 32803 inter-ligation reads, 106 candidate loops.
2023-06-25 17:48:49 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 2301700 self-ligation reads and 29014 inter-ligation reads, 92 candidate loops.
2023-06-25 17:48:49 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 2284798 self-ligation reads and 39459 inter-ligation reads, 137 candidate loops.
2023-06-25 17:48:54 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 2603324 self-ligation reads and 20381 inter-ligation reads, 91 candidate loops.
2023-06-25 17:49:04 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 2520384 self-ligation reads and 30162 inter-ligation reads, 114 candidate loops.
2023-06-25 17:49:13 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 2446023 self-ligation reads and 41055 inter-ligation reads, 112 candidate loops.
2023-06-25 17:49:47 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 2822271 self-ligation reads and 33714 inter-ligation reads, 118 candidate loops.
2023-06-25 17:50:04 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 2872127 self-ligation reads and 30865 inter-ligation reads, 104 candidate loops.
2023-06-25 17:50:34 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 3318580 self-ligation reads and 50268 inter-ligation reads, 140 candidate loops.
2023-06-25 17:50:39 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 3336907 self-ligation reads and 32926 inter-ligation reads, 129 candidate loops.
2023-06-25 17:50:40 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 3244561 self-ligation reads and 45791 inter-ligation reads, 173 candidate loops.
2023-06-25 17:50:50 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 3198002 self-ligation reads and 53510 inter-ligation reads, 168 candidate loops.
2023-06-25 17:51:21 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 3731451 self-ligation reads and 72547 inter-ligation reads, 242 candidate loops.
2023-06-25 17:52:15 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 3995998 self-ligation reads and 63986 inter-ligation reads, 210 candidate loops.
2023-06-25 17:52:23 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 4197506 self-ligation reads and 74877 inter-ligation reads, 245 candidate loops.
2023-06-25 17:53:03 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 4221847 self-ligation reads and 65522 inter-ligation reads, 226 candidate loops.
2023-06-25 17:53:07 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 4626569 self-ligation reads and 69814 inter-ligation reads, 224 candidate loops.
2023-06-25 17:57:39 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 6519146 self-ligation reads and 117461 inter-ligation reads, 347 candidate loops.
2023-06-25 17:57:52 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 71364 for eps=10000,minPts=100
2023-06-25 17:57:54 cLoops2 INFO Clustering chrY and chrY using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:54 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:57:55 cLoops2 INFO Clustering chr16 and chr16 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:55 cLoops2 INFO Clustering chrX and chrX using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:55 cLoops2 INFO Clustering chr19 and chr19 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:55 cLoops2 INFO Clustering chr18 and chr18 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr15 and chr15 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr10 and chr10 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr13 and chr13 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr14 and chr14 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr12 and chr12 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr3 and chr3 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr8 and chr8 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr17 and chr17 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr9 and chr9 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr6 and chr6 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr11 and chr11 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr5 and chr5 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr4 and chr4 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:57 cLoops2 INFO Clustering chr2 and chr2 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:57 cLoops2 INFO Clustering chr7 and chr7 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:57 cLoops2 INFO Clustering chr1 and chr1 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:58:38 cLoops2 INFO Clustering chrX and chrX finished. Estimated 0 self-ligation reads and 9324 inter-ligation reads, 69 candidate loops.
2023-06-25 17:58:57 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 15607 self-ligation reads and 100736 inter-ligation reads, 350 candidate loops.
2023-06-25 17:59:11 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 7688 self-ligation reads and 81237 inter-ligation reads, 292 candidate loops.
2023-06-25 17:59:14 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 33128 self-ligation reads and 122412 inter-ligation reads, 452 candidate loops.
2023-06-25 17:59:19 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 13109 self-ligation reads and 113936 inter-ligation reads, 416 candidate loops.
2023-06-25 17:59:23 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 2566 self-ligation reads and 104095 inter-ligation reads, 453 candidate loops.
2023-06-25 17:59:25 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 1558 self-ligation reads and 67810 inter-ligation reads, 361 candidate loops.
2023-06-25 17:59:29 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 10555 self-ligation reads and 121143 inter-ligation reads, 438 candidate loops.
2023-06-25 17:59:37 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 24464 self-ligation reads and 96312 inter-ligation reads, 381 candidate loops.
2023-06-25 17:59:37 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 49306 self-ligation reads and 167757 inter-ligation reads, 609 candidate loops.
2023-06-25 17:59:39 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 3683 self-ligation reads and 142531 inter-ligation reads, 605 candidate loops.
2023-06-25 17:59:41 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 13194 self-ligation reads and 153104 inter-ligation reads, 573 candidate loops.
2023-06-25 17:59:41 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 4534 self-ligation reads and 104119 inter-ligation reads, 423 candidate loops.
2023-06-25 17:59:48 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 58707 self-ligation reads and 138604 inter-ligation reads, 592 candidate loops.
2023-06-25 17:59:52 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 35085 self-ligation reads and 252146 inter-ligation reads, 827 candidate loops.
2023-06-25 17:59:53 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 15049 self-ligation reads and 231120 inter-ligation reads, 837 candidate loops.
2023-06-25 18:00:02 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 23610 self-ligation reads and 201542 inter-ligation reads, 696 candidate loops.
2023-06-25 18:00:14 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 56207 self-ligation reads and 233382 inter-ligation reads, 878 candidate loops.
2023-06-25 18:00:14 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 23056 self-ligation reads and 238494 inter-ligation reads, 833 candidate loops.

Based on the log, I think maybe the loops were actually called, but the loop files failed to be generated for unknown reasons. Any suggestions?

Thank you, Yaqiang!

Best,
Charles

[YaqiangCao]

I tried to call loops after deleting the .ixy files with chromosomes like chrUn_random and chrUn_random in the cLoops2 data folders and then updated the .json file by cLoops2 update. But the error message is the same and no loop files were generated.

The error message is:

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 34, 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

The cLoops2.log is:

2023-06-25 16:42:37 cLoops2 INFO Command: cLoops2 callLoops -d ./01.cLoops2.2 -eps 2500,5000,10000 -minPts 25,50,100 -p 50 -o ./01.cLoops2.2 -cut 1000 -mcut -1 -filter False -i True -j True -w True -hic True -max_cut False -trans False -emPair False

2023-06-25 16:42:37 cLoops2 INFO -hic option selected, cDBSCAN2 is used instead of blockDBSCAN.
2023-06-25 16:42:38 cLoops2 INFO Clustering chrM and chrM using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:38 cLoops2 INFO Clustering chrY and chrY using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:38 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 16:42:38 cLoops2 INFO Clustering chrM and chrM finished. Estimated 386 self-ligation reads and 503 inter-ligation reads, 1 candidate loops.
2023-06-25 16:42:39 cLoops2 INFO Clustering chrX and chrX using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:39 cLoops2 INFO Clustering chr10 and chr10 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:39 cLoops2 INFO Clustering chr19 and chr19 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr18 and chr18 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr16 and chr16 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr17 and chr17 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr15 and chr15 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr12 and chr12 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr13 and chr13 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr11 and chr11 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:40 cLoops2 INFO Clustering chr14 and chr14 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr6 and chr6 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr5 and chr5 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr3 and chr3 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr9 and chr9 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:41 cLoops2 INFO Clustering chr2 and chr2 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:42 cLoops2 INFO Clustering chr4 and chr4 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:42 cLoops2 INFO Clustering chr7 and chr7 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:42 cLoops2 INFO Clustering chr8 and chr8 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:42:45 cLoops2 INFO Clustering chr1 and chr1 using eps 2500, minPts 100,pre-set distance cutoff > 1000
2023-06-25 16:44:09 cLoops2 INFO Clustering chrX and chrX finished. Estimated 104503 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 16:49:08 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 2111177 self-ligation reads and 4561 inter-ligation reads, 28 candidate loops.
2023-06-25 16:50:23 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 2240217 self-ligation reads and 7719 inter-ligation reads, 45 candidate loops.
2023-06-25 16:50:54 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 2506965 self-ligation reads and 10640 inter-ligation reads, 47 candidate loops.
2023-06-25 16:51:02 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 2428547 self-ligation reads and 5898 inter-ligation reads, 39 candidate loops.
2023-06-25 16:51:42 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 2530786 self-ligation reads and 6593 inter-ligation reads, 38 candidate loops.
2023-06-25 16:52:19 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 2337032 self-ligation reads and 4623 inter-ligation reads, 30 candidate loops.
2023-06-25 16:53:03 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 2579736 self-ligation reads and 6752 inter-ligation reads, 44 candidate loops.
2023-06-25 16:53:46 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 3079319 self-ligation reads and 8669 inter-ligation reads, 58 candidate loops.
2023-06-25 16:53:57 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 2773870 self-ligation reads and 5556 inter-ligation reads, 38 candidate loops.
2023-06-25 16:54:37 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 3605355 self-ligation reads and 19631 inter-ligation reads, 98 candidate loops.
2023-06-25 16:55:49 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 3639109 self-ligation reads and 17682 inter-ligation reads, 54 candidate loops.
2023-06-25 16:55:51 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 3523667 self-ligation reads and 13122 inter-ligation reads, 77 candidate loops.
2023-06-25 16:56:19 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 3518936 self-ligation reads and 5822 inter-ligation reads, 37 candidate loops.
2023-06-25 16:57:08 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 4912785 self-ligation reads and 11592 inter-ligation reads, 52 candidate loops.
2023-06-25 16:57:09 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 4339006 self-ligation reads and 11463 inter-ligation reads, 69 candidate loops.
2023-06-25 16:57:58 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 4463507 self-ligation reads and 14674 inter-ligation reads, 84 candidate loops.
2023-06-25 16:58:04 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 4889701 self-ligation reads and 17885 inter-ligation reads, 93 candidate loops.
2023-06-25 17:00:27 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 5011907 self-ligation reads and 12476 inter-ligation reads, 71 candidate loops.
2023-06-25 17:06:04 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 7872768 self-ligation reads and 34178 inter-ligation reads, 172 candidate loops.
2023-06-25 17:06:18 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 9824 for eps=2500,minPts=100
2023-06-25 17:06:20 cLoops2 INFO Clustering chrM and chrM using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:20 cLoops2 INFO Clustering chrY and chrY using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:20 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:06:20 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 277 inter-ligation reads, 1 candidate loops.
2023-06-25 17:06:21 cLoops2 INFO Clustering chr17 and chr17 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chrX and chrX using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chr19 and chr19 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chr18 and chr18 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:21 cLoops2 INFO Clustering chr16 and chr16 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr2 and chr2 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr15 and chr15 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr13 and chr13 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr14 and chr14 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr3 and chr3 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr12 and chr12 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr8 and chr8 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr10 and chr10 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr11 and chr11 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:22 cLoops2 INFO Clustering chr9 and chr9 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr5 and chr5 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr4 and chr4 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr7 and chr7 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:23 cLoops2 INFO Clustering chr6 and chr6 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:06:26 cLoops2 INFO Clustering chr1 and chr1 using eps 2500, minPts 50,pre-set distance cutoff > 9824
2023-06-25 17:07:16 cLoops2 INFO Clustering chrX and chrX finished. Estimated 0 self-ligation reads and 1950 inter-ligation reads, 4 candidate loops.
2023-06-25 17:07:35 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 0 self-ligation reads and 6283 inter-ligation reads, 53 candidate loops.
2023-06-25 17:07:52 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 0 self-ligation reads and 11811 inter-ligation reads, 84 candidate loops.
2023-06-25 17:07:55 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 0 self-ligation reads and 5915 inter-ligation reads, 43 candidate loops.
2023-06-25 17:07:57 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 0 self-ligation reads and 3631 inter-ligation reads, 36 candidate loops.
2023-06-25 17:07:59 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 0 self-ligation reads and 7011 inter-ligation reads, 53 candidate loops.
2023-06-25 17:08:05 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 0 self-ligation reads and 3973 inter-ligation reads, 43 candidate loops.
2023-06-25 17:08:07 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 0 self-ligation reads and 7700 inter-ligation reads, 55 candidate loops.
2023-06-25 17:08:12 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 0 self-ligation reads and 9846 inter-ligation reads, 102 candidate loops.
2023-06-25 17:08:17 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 864 self-ligation reads and 15100 inter-ligation reads, 64 candidate loops.
2023-06-25 17:08:18 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 0 self-ligation reads and 6909 inter-ligation reads, 61 candidate loops.
2023-06-25 17:08:20 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 0 self-ligation reads and 30128 inter-ligation reads, 201 candidate loops.
2023-06-25 17:08:26 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 0 self-ligation reads and 5139 inter-ligation reads, 49 candidate loops.
2023-06-25 17:08:27 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 1062 self-ligation reads and 16496 inter-ligation reads, 138 candidate loops.
2023-06-25 17:08:29 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 380 self-ligation reads and 20780 inter-ligation reads, 167 candidate loops.
2023-06-25 17:08:35 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 0 self-ligation reads and 12440 inter-ligation reads, 107 candidate loops.
2023-06-25 17:08:35 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 28739 self-ligation reads and 19853 inter-ligation reads, 152 candidate loops.
2023-06-25 17:08:40 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 910 self-ligation reads and 19578 inter-ligation reads, 166 candidate loops.
2023-06-25 17:08:44 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 0 self-ligation reads and 13187 inter-ligation reads, 108 candidate loops.
2023-06-25 17:09:38 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 919 self-ligation reads and 43564 inter-ligation reads, 320 candidate loops.
2023-06-25 17:09:41 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 7938 for eps=2500,minPts=50
2023-06-25 17:09:41 cLoops2 INFO Clustering chrM and chrM using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:41 cLoops2 INFO Clustering chrY and chrY using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:41 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:09:41 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 411 inter-ligation reads, 1 candidate loops.
2023-06-25 17:09:42 cLoops2 INFO Clustering chr16 and chr16 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chr19 and chr19 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chrX and chrX using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chr18 and chr18 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:42 cLoops2 INFO Clustering chr15 and chr15 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr10 and chr10 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr13 and chr13 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr2 and chr2 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr6 and chr6 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr9 and chr9 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr8 and chr8 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr17 and chr17 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr1 and chr1 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr4 and chr4 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr11 and chr11 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr14 and chr14 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr5 and chr5 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:43 cLoops2 INFO Clustering chr12 and chr12 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:44 cLoops2 INFO Clustering chr3 and chr3 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:09:44 cLoops2 INFO Clustering chr7 and chr7 using eps 2500, minPts 25,pre-set distance cutoff > 7938
2023-06-25 17:10:26 cLoops2 INFO Clustering chrX and chrX finished. Estimated 2485 self-ligation reads and 2571 inter-ligation reads, 58 candidate loops.
2023-06-25 17:11:20 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 47906 self-ligation reads and 92013 inter-ligation reads, 1621 candidate loops.
2023-06-25 17:11:31 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 18005 self-ligation reads and 73569 inter-ligation reads, 1359 candidate loops.
2023-06-25 17:11:48 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 62753 self-ligation reads and 122493 inter-ligation reads, 2017 candidate loops.
2023-06-25 17:11:52 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 47580 self-ligation reads and 100371 inter-ligation reads, 1825 candidate loops.
2023-06-25 17:11:52 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 40487 self-ligation reads and 77739 inter-ligation reads, 1417 candidate loops.
2023-06-25 17:11:55 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 5986 self-ligation reads and 64437 inter-ligation reads, 1341 candidate loops.
2023-06-25 17:12:23 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 41121 self-ligation reads and 110178 inter-ligation reads, 1902 candidate loops.
2023-06-25 17:12:38 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 29873 self-ligation reads and 77886 inter-ligation reads, 1454 candidate loops.
2023-06-25 17:12:44 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 57808 self-ligation reads and 102883 inter-ligation reads, 1868 candidate loops.
2023-06-25 17:13:11 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 127940 self-ligation reads and 156111 inter-ligation reads, 2557 candidate loops.
2023-06-25 17:13:12 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 38895 self-ligation reads and 142632 inter-ligation reads, 2509 candidate loops.
2023-06-25 17:13:15 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 37326 self-ligation reads and 125331 inter-ligation reads, 2442 candidate loops.
2023-06-25 17:13:16 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 123767 self-ligation reads and 141381 inter-ligation reads, 2407 candidate loops.
2023-06-25 17:13:59 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 86652 self-ligation reads and 199175 inter-ligation reads, 3396 candidate loops.
2023-06-25 17:14:12 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 163026 self-ligation reads and 230874 inter-ligation reads, 3893 candidate loops.
2023-06-25 17:14:18 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 89766 self-ligation reads and 207738 inter-ligation reads, 3563 candidate loops.
2023-06-25 17:14:34 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 145548 self-ligation reads and 229686 inter-ligation reads, 3891 candidate loops.
2023-06-25 17:14:40 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 75598 self-ligation reads and 211767 inter-ligation reads, 3807 candidate loops.
2023-06-25 17:17:35 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 309812 self-ligation reads and 360314 inter-ligation reads, 5879 candidate loops.
2023-06-25 17:17:38 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 7143 for eps=2500,minPts=25
2023-06-25 17:17:39 cLoops2 INFO Clustering chrY and chrY using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:39 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:17:39 cLoops2 INFO Clustering chrM and chrM using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:39 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 448 inter-ligation reads, 1 candidate loops.
2023-06-25 17:17:39 cLoops2 INFO Clustering chr18 and chr18 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:39 cLoops2 INFO Clustering chrX and chrX using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr14 and chr14 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr8 and chr8 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr4 and chr4 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr17 and chr17 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr15 and chr15 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr19 and chr19 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr13 and chr13 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:40 cLoops2 INFO Clustering chr10 and chr10 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr9 and chr9 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr6 and chr6 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr7 and chr7 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr3 and chr3 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr5 and chr5 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr16 and chr16 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr12 and chr12 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:41 cLoops2 INFO Clustering chr11 and chr11 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:44 cLoops2 INFO Clustering chr2 and chr2 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:17:44 cLoops2 INFO Clustering chr1 and chr1 using eps 5000, minPts 100,pre-set distance cutoff > 7143
2023-06-25 17:18:23 cLoops2 INFO Clustering chrX and chrX finished. Estimated 2928 self-ligation reads and 463 inter-ligation reads, 3 candidate loops.
2023-06-25 17:18:54 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 64378 self-ligation reads and 31924 inter-ligation reads, 195 candidate loops.
2023-06-25 17:19:07 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 27245 self-ligation reads and 24414 inter-ligation reads, 152 candidate loops.
2023-06-25 17:19:18 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 8263 self-ligation reads and 17617 inter-ligation reads, 112 candidate loops.
2023-06-25 17:19:20 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 84460 self-ligation reads and 47459 inter-ligation reads, 272 candidate loops.
2023-06-25 17:19:21 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 65070 self-ligation reads and 29851 inter-ligation reads, 193 candidate loops.
2023-06-25 17:19:24 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 56852 self-ligation reads and 40457 inter-ligation reads, 251 candidate loops.
2023-06-25 17:19:26 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 56136 self-ligation reads and 24836 inter-ligation reads, 154 candidate loops.
2023-06-25 17:19:29 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 77574 self-ligation reads and 35350 inter-ligation reads, 227 candidate loops.
2023-06-25 17:19:31 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 39652 self-ligation reads and 24940 inter-ligation reads, 152 candidate loops.
2023-06-25 17:19:40 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 55836 self-ligation reads and 47060 inter-ligation reads, 264 candidate loops.
2023-06-25 17:19:44 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 49750 self-ligation reads and 31799 inter-ligation reads, 223 candidate loops.
2023-06-25 17:19:52 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 157716 self-ligation reads and 51655 inter-ligation reads, 298 candidate loops.
2023-06-25 17:19:54 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 168552 self-ligation reads and 65937 inter-ligation reads, 354 candidate loops.
2023-06-25 17:20:12 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 120714 self-ligation reads and 71633 inter-ligation reads, 461 candidate loops.
2023-06-25 17:20:14 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 211831 self-ligation reads and 86278 inter-ligation reads, 512 candidate loops.
2023-06-25 17:20:25 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 130276 self-ligation reads and 72665 inter-ligation reads, 477 candidate loops.
2023-06-25 17:20:30 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 197924 self-ligation reads and 84823 inter-ligation reads, 501 candidate loops.
2023-06-25 17:20:35 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 105113 self-ligation reads and 68633 inter-ligation reads, 425 candidate loops.
2023-06-25 17:22:09 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 417345 self-ligation reads and 138165 inter-ligation reads, 783 candidate loops.
2023-06-25 17:22:12 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 6298 for eps=5000,minPts=100
2023-06-25 17:22:13 cLoops2 INFO Clustering chrY and chrY using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:13 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:22:13 cLoops2 INFO Clustering chrM and chrM using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:13 cLoops2 INFO Clustering chrM and chrM finished. Estimated 0 self-ligation reads and 475 inter-ligation reads, 1 candidate loops.
2023-06-25 17:22:14 cLoops2 INFO Clustering chr15 and chr15 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chrX and chrX using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr18 and chr18 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr17 and chr17 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr16 and chr16 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr4 and chr4 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr19 and chr19 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:14 cLoops2 INFO Clustering chr10 and chr10 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr13 and chr13 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr14 and chr14 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr3 and chr3 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr9 and chr9 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr8 and chr8 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr6 and chr6 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr7 and chr7 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr12 and chr12 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr5 and chr5 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:15 cLoops2 INFO Clustering chr11 and chr11 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:16 cLoops2 INFO Clustering chr2 and chr2 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:22:17 cLoops2 INFO Clustering chr1 and chr1 using eps 5000, minPts 50,pre-set distance cutoff > 6298
2023-06-25 17:23:05 cLoops2 INFO Clustering chrX and chrX finished. Estimated 16653 self-ligation reads and 7951 inter-ligation reads, 112 candidate loops.
2023-06-25 17:24:17 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 504305 self-ligation reads and 58623 inter-ligation reads, 599 candidate loops.
2023-06-25 17:24:54 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 592410 self-ligation reads and 77901 inter-ligation reads, 743 candidate loops.
2023-06-25 17:25:00 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 427355 self-ligation reads and 73505 inter-ligation reads, 845 candidate loops.
2023-06-25 17:25:20 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 545938 self-ligation reads and 62948 inter-ligation reads, 655 candidate loops.
2023-06-25 17:25:21 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 551508 self-ligation reads and 80876 inter-ligation reads, 853 candidate loops.
2023-06-25 17:25:44 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 480534 self-ligation reads and 74481 inter-ligation reads, 867 candidate loops.
2023-06-25 17:26:12 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 611982 self-ligation reads and 98902 inter-ligation reads, 1035 candidate loops.
2023-06-25 17:26:19 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 463886 self-ligation reads and 92361 inter-ligation reads, 1181 candidate loops.
2023-06-25 17:26:19 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 481358 self-ligation reads and 90829 inter-ligation reads, 1060 candidate loops.
2023-06-25 17:26:31 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 831678 self-ligation reads and 116667 inter-ligation reads, 1027 candidate loops.
2023-06-25 17:26:46 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 739789 self-ligation reads and 88473 inter-ligation reads, 1019 candidate loops.
2023-06-25 17:26:48 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 806691 self-ligation reads and 109282 inter-ligation reads, 1105 candidate loops.
2023-06-25 17:26:57 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 776988 self-ligation reads and 109470 inter-ligation reads, 1139 candidate loops.
2023-06-25 17:27:00 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 1235231 self-ligation reads and 141234 inter-ligation reads, 1227 candidate loops.
2023-06-25 17:27:09 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 986027 self-ligation reads and 126541 inter-ligation reads, 1242 candidate loops.
2023-06-25 17:27:29 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 1006039 self-ligation reads and 126547 inter-ligation reads, 1258 candidate loops.
2023-06-25 17:27:42 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 1157184 self-ligation reads and 139360 inter-ligation reads, 1252 candidate loops.
2023-06-25 17:28:21 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 1124564 self-ligation reads and 146249 inter-ligation reads, 1500 candidate loops.
2023-06-25 17:30:24 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 1867887 self-ligation reads and 212919 inter-ligation reads, 1817 candidate loops.
2023-06-25 17:30:30 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 5162 for eps=5000,minPts=50
2023-06-25 17:30:31 cLoops2 INFO Clustering chrY and chrY using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:31 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:30:31 cLoops2 INFO Clustering chrM and chrM using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:31 cLoops2 INFO Clustering chrM and chrM finished. Estimated 498 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:30:32 cLoops2 INFO Clustering chrX and chrX using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr12 and chr12 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr19 and chr19 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr6 and chr6 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr18 and chr18 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:32 cLoops2 INFO Clustering chr17 and chr17 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr15 and chr15 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr13 and chr13 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr14 and chr14 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr3 and chr3 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr16 and chr16 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr11 and chr11 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:33 cLoops2 INFO Clustering chr7 and chr7 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr10 and chr10 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr4 and chr4 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr9 and chr9 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:34 cLoops2 INFO Clustering chr8 and chr8 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:35 cLoops2 INFO Clustering chr5 and chr5 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:35 cLoops2 INFO Clustering chr1 and chr1 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:30:35 cLoops2 INFO Clustering chr2 and chr2 using eps 5000, minPts 25,pre-set distance cutoff > 5162
2023-06-25 17:32:12 cLoops2 INFO Clustering chrX and chrX finished. Estimated 225876 self-ligation reads and 35518 inter-ligation reads, 994 candidate loops.
2023-06-25 17:33:18 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 1019542 self-ligation reads and 79609 inter-ligation reads, 1095 candidate loops.
2023-06-25 17:34:10 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 1047853 self-ligation reads and 95191 inter-ligation reads, 1392 candidate loops.
2023-06-25 17:34:23 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 1214445 self-ligation reads and 120818 inter-ligation reads, 1604 candidate loops.
2023-06-25 17:34:41 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 1179767 self-ligation reads and 108230 inter-ligation reads, 1565 candidate loops.
2023-06-25 17:34:44 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 1258567 self-ligation reads and 115264 inter-ligation reads, 1623 candidate loops.
2023-06-25 17:35:00 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 1277419 self-ligation reads and 96596 inter-ligation reads, 1505 candidate loops.
2023-06-25 17:35:14 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 1257134 self-ligation reads and 99499 inter-ligation reads, 1681 candidate loops.
2023-06-25 17:35:33 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 1438140 self-ligation reads and 125750 inter-ligation reads, 1792 candidate loops.
2023-06-25 17:36:02 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 1705257 self-ligation reads and 153035 inter-ligation reads, 2147 candidate loops.
2023-06-25 17:36:03 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 1676018 self-ligation reads and 171429 inter-ligation reads, 2140 candidate loops.
2023-06-25 17:36:09 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 1724178 self-ligation reads and 144374 inter-ligation reads, 1894 candidate loops.
2023-06-25 17:36:24 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 1677707 self-ligation reads and 138430 inter-ligation reads, 2295 candidate loops.
2023-06-25 17:36:38 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 1337696 self-ligation reads and 131550 inter-ligation reads, 2186 candidate loops.
2023-06-25 17:36:39 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 2333323 self-ligation reads and 186306 inter-ligation reads, 2173 candidate loops.
2023-06-25 17:36:44 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 1989989 self-ligation reads and 185087 inter-ligation reads, 2505 candidate loops.
2023-06-25 17:37:25 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 2101063 self-ligation reads and 187947 inter-ligation reads, 2552 candidate loops.
2023-06-25 17:37:58 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 2421585 self-ligation reads and 200858 inter-ligation reads, 2807 candidate loops.
2023-06-25 17:37:59 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 2254391 self-ligation reads and 217258 inter-ligation reads, 2894 candidate loops.
2023-06-25 17:41:35 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 3483648 self-ligation reads and 351894 inter-ligation reads, 4188 candidate loops.
2023-06-25 17:41:43 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 2586 for eps=5000,minPts=25
2023-06-25 17:41:44 cLoops2 INFO Clustering chrY and chrY using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:44 cLoops2 INFO Clustering chrM and chrM using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:44 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:41:44 cLoops2 INFO Clustering chrM and chrM finished. Estimated 635 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:41:45 cLoops2 INFO Clustering chr19 and chr19 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:45 cLoops2 INFO Clustering chrX and chrX using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:45 cLoops2 INFO Clustering chr14 and chr14 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:45 cLoops2 INFO Clustering chr12 and chr12 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr18 and chr18 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr17 and chr17 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr13 and chr13 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:46 cLoops2 INFO Clustering chr3 and chr3 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr16 and chr16 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr9 and chr9 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr15 and chr15 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr6 and chr6 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr10 and chr10 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr7 and chr7 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr11 and chr11 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr5 and chr5 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:47 cLoops2 INFO Clustering chr8 and chr8 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:48 cLoops2 INFO Clustering chr4 and chr4 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:49 cLoops2 INFO Clustering chr1 and chr1 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:41:49 cLoops2 INFO Clustering chr2 and chr2 using eps 10000, minPts 100,pre-set distance cutoff > 2586
2023-06-25 17:43:56 cLoops2 INFO Clustering chrX and chrX finished. Estimated 627752 self-ligation reads and 3499 inter-ligation reads, 17 candidate loops.
2023-06-25 17:47:22 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 1871918 self-ligation reads and 27254 inter-ligation reads, 100 candidate loops.
2023-06-25 17:47:55 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 2112366 self-ligation reads and 32803 inter-ligation reads, 106 candidate loops.
2023-06-25 17:48:49 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 2301700 self-ligation reads and 29014 inter-ligation reads, 92 candidate loops.
2023-06-25 17:48:49 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 2284798 self-ligation reads and 39459 inter-ligation reads, 137 candidate loops.
2023-06-25 17:48:54 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 2603324 self-ligation reads and 20381 inter-ligation reads, 91 candidate loops.
2023-06-25 17:49:04 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 2520384 self-ligation reads and 30162 inter-ligation reads, 114 candidate loops.
2023-06-25 17:49:13 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 2446023 self-ligation reads and 41055 inter-ligation reads, 112 candidate loops.
2023-06-25 17:49:47 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 2822271 self-ligation reads and 33714 inter-ligation reads, 118 candidate loops.
2023-06-25 17:50:04 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 2872127 self-ligation reads and 30865 inter-ligation reads, 104 candidate loops.
2023-06-25 17:50:34 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 3318580 self-ligation reads and 50268 inter-ligation reads, 140 candidate loops.
2023-06-25 17:50:39 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 3336907 self-ligation reads and 32926 inter-ligation reads, 129 candidate loops.
2023-06-25 17:50:40 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 3244561 self-ligation reads and 45791 inter-ligation reads, 173 candidate loops.
2023-06-25 17:50:50 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 3198002 self-ligation reads and 53510 inter-ligation reads, 168 candidate loops.
2023-06-25 17:51:21 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 3731451 self-ligation reads and 72547 inter-ligation reads, 242 candidate loops.
2023-06-25 17:52:15 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 3995998 self-ligation reads and 63986 inter-ligation reads, 210 candidate loops.
2023-06-25 17:52:23 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 4197506 self-ligation reads and 74877 inter-ligation reads, 245 candidate loops.
2023-06-25 17:53:03 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 4221847 self-ligation reads and 65522 inter-ligation reads, 226 candidate loops.
2023-06-25 17:53:07 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 4626569 self-ligation reads and 69814 inter-ligation reads, 224 candidate loops.
2023-06-25 17:57:39 cLoops2 INFO Clustering chr1 and chr1 finished. Estimated 6519146 self-ligation reads and 117461 inter-ligation reads, 347 candidate loops.
2023-06-25 17:57:52 cLoops2 INFO Estimated inter-ligation and self-ligation distance cutoff > 71364 for eps=10000,minPts=100
2023-06-25 17:57:54 cLoops2 INFO Clustering chrY and chrY using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:54 cLoops2 INFO Clustering chrY and chrY finished. Estimated 0 self-ligation reads and 0 inter-ligation reads, 0 candidate loops.
2023-06-25 17:57:55 cLoops2 INFO Clustering chr16 and chr16 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:55 cLoops2 INFO Clustering chrX and chrX using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:55 cLoops2 INFO Clustering chr19 and chr19 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:55 cLoops2 INFO Clustering chr18 and chr18 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr15 and chr15 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr10 and chr10 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr13 and chr13 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr14 and chr14 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr12 and chr12 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr3 and chr3 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr8 and chr8 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr17 and chr17 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr9 and chr9 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr6 and chr6 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr11 and chr11 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr5 and chr5 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:56 cLoops2 INFO Clustering chr4 and chr4 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:57 cLoops2 INFO Clustering chr2 and chr2 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:57 cLoops2 INFO Clustering chr7 and chr7 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:57:57 cLoops2 INFO Clustering chr1 and chr1 using eps 10000, minPts 50,pre-set distance cutoff > 71364
2023-06-25 17:58:38 cLoops2 INFO Clustering chrX and chrX finished. Estimated 0 self-ligation reads and 9324 inter-ligation reads, 69 candidate loops.
2023-06-25 17:58:57 cLoops2 INFO Clustering chr19 and chr19 finished. Estimated 15607 self-ligation reads and 100736 inter-ligation reads, 350 candidate loops.
2023-06-25 17:59:11 cLoops2 INFO Clustering chr18 and chr18 finished. Estimated 7688 self-ligation reads and 81237 inter-ligation reads, 292 candidate loops.
2023-06-25 17:59:14 cLoops2 INFO Clustering chr17 and chr17 finished. Estimated 33128 self-ligation reads and 122412 inter-ligation reads, 452 candidate loops.
2023-06-25 17:59:19 cLoops2 INFO Clustering chr16 and chr16 finished. Estimated 13109 self-ligation reads and 113936 inter-ligation reads, 416 candidate loops.
2023-06-25 17:59:23 cLoops2 INFO Clustering chr10 and chr10 finished. Estimated 2566 self-ligation reads and 104095 inter-ligation reads, 453 candidate loops.
2023-06-25 17:59:25 cLoops2 INFO Clustering chr13 and chr13 finished. Estimated 1558 self-ligation reads and 67810 inter-ligation reads, 361 candidate loops.
2023-06-25 17:59:29 cLoops2 INFO Clustering chr15 and chr15 finished. Estimated 10555 self-ligation reads and 121143 inter-ligation reads, 438 candidate loops.
2023-06-25 17:59:37 cLoops2 INFO Clustering chr14 and chr14 finished. Estimated 24464 self-ligation reads and 96312 inter-ligation reads, 381 candidate loops.
2023-06-25 17:59:37 cLoops2 INFO Clustering chr12 and chr12 finished. Estimated 49306 self-ligation reads and 167757 inter-ligation reads, 609 candidate loops.
2023-06-25 17:59:39 cLoops2 INFO Clustering chr6 and chr6 finished. Estimated 3683 self-ligation reads and 142531 inter-ligation reads, 605 candidate loops.
2023-06-25 17:59:41 cLoops2 INFO Clustering chr9 and chr9 finished. Estimated 13194 self-ligation reads and 153104 inter-ligation reads, 573 candidate loops.
2023-06-25 17:59:41 cLoops2 INFO Clustering chr3 and chr3 finished. Estimated 4534 self-ligation reads and 104119 inter-ligation reads, 423 candidate loops.
2023-06-25 17:59:48 cLoops2 INFO Clustering chr8 and chr8 finished. Estimated 58707 self-ligation reads and 138604 inter-ligation reads, 592 candidate loops.
2023-06-25 17:59:52 cLoops2 INFO Clustering chr11 and chr11 finished. Estimated 35085 self-ligation reads and 252146 inter-ligation reads, 827 candidate loops.
2023-06-25 17:59:53 cLoops2 INFO Clustering chr7 and chr7 finished. Estimated 15049 self-ligation reads and 231120 inter-ligation reads, 837 candidate loops.
2023-06-25 18:00:02 cLoops2 INFO Clustering chr5 and chr5 finished. Estimated 23610 self-ligation reads and 201542 inter-ligation reads, 696 candidate loops.
2023-06-25 18:00:14 cLoops2 INFO Clustering chr4 and chr4 finished. Estimated 56207 self-ligation reads and 233382 inter-ligation reads, 878 candidate loops.
2023-06-25 18:00:14 cLoops2 INFO Clustering chr2 and chr2 finished. Estimated 23056 self-ligation reads and 238494 inter-ligation reads, 833 candidate loops.
Based on the log, I think maybe the loops were actually called, but the loop files failed to be generated for unknown reasons. Any suggestions?

Thank you, Yaqiang!

Best, Charles

option 1: remove chrY, chrM and then try again with a small chromosome first, create a directory, copy chr21 to it, cLoops2 update it, call loops with simple parameters, such as -minPts 5000 -eps 25,50
option 2: check in the genome browser/juicebox to see if you can see some loops. If you can see, use that region as to optimize -minPts and -eps; smaller eps, the loops anchors are smaller; higher minPts, more confident the loops are (fewer loops).

[YaqiangCao]

or just chr19 as test as it seems your data are from mice.

[CW20221031]

Thank you Yaqiang! chr19 works! I used -minPts 5000 -eps 25,50 for chr19 and it calls 160 loops. I will try to remove chrM and chrY to call loops for the whole genome. Thanks!

[YaqiangCao]

Thank you Yaqiang! chr19 works! I used -minPts 5000 -eps 25,50 for chr19 and it calls 160 loops. I will try to remove chrM and chrY to call loops for the whole genome. Thanks!

You can visualize the loops in juicebox (-j option) or washU (-w option) to check those loops. Then decide if the loop anchors are too broad or the loop strength are too little to change -minPts and -eps .

[CW20221031]

Thank you! Will do.