StripePy

---

StripePy is a CLI application written in Python that recognizes architectural stripes found in the interaction matrix files generated by Chromosome Conformation Capture experiments, such as Hi-C and Micro-C. Matrix files in .cool, .mcool, and .hic (including .hic v9 files) are supported.

StripePy is developed on Linux and macOS and is also tested on Windows.

Installing StripePy

Installing with pip

pip install 'stripepy-hic[all]'

Installing with conda

conda create -n stripepy -c conda-forge -c bioconda stripepy-hic

Installing from source

Instructions for Linux and macOS:

# create and activate a venv (optional)
python3 -m venv venv
. venv/bin/activate

# get StripePy source code
git clone https://github.com/paulsengroup/StripePy.git

# optional, checkout a specific version
# git checkout v0.0.2

# install StripePy
cd StripePy
pip install '.[all]'

# ensure StripePy is in your PATH
stripepy --help

Instructions for Windows

# create and activate a venv (optional)
python3 -m venv venv
venv\Scripts\activate

# get StripePy source code
git clone https://github.com/paulsengroup/StripePy.git

# optional, checkout a specific version
# git checkout v0.0.2

# install StripePy
cd StripePy
pip install .

# ensure StripePy is in your PATH
stripepy --help

Running StripePy

StripePy is organized into a few subcommands:

• stripepy call: run the stripe detection algorithm and store the identified stripes in a .hdf5 file.
• stripepy view: take the result.hdf5 file generated by stripepy call and extract stripes in BEDPE format.
• stripepy plot: generate various kinds of plots to inspect the stripes identified by stripepy call.
• stripepy download: download a minified sample dataset suitable to quickly test StripePy.

Walkthrough

The following is an example of a typical run of StripePy. The steps outlined in this section assume that StripePy is running on a UNIX system. Some commands may need some tweaking to run on Windows.

1) Download a sample dataset

This step is optional. Feel free to use your own interaction matrix (make sure the matrix is in .cool, .mcool, or .hic format).

# This may take a while on slow internet connections
user@dev:/tmp$ stripepy download --name 4DNFI9GMP2J8

2025-01-14 12:46:01.304277 [info     ] downloading dataset "4DNFI9GMP2J8" (assembly=hg38)...
2025-01-14 12:46:23.900411 [info     ] DONE! Downloading dataset "4DNFI9GMP2J8" took 22.596s.
2025-01-14 12:46:23.901141 [info     ] computing MD5 digest for file "/tmp/4DNFI9GMP2J8.dvizz7v1"...
2025-01-14 12:46:24.050566 [info     ] MD5 checksum match!
2025-01-14 12:46:24.050695 [info     ] successfully downloaded dataset "https://zenodo.org/records/14643417/files/4DNFI9GMP2J8.stripepy.mcool?download=1" to file "4DNFI9GMP2J8.mcool"
2025-01-14 12:46:24.050752 [info     ] file size: 106.84MB. Elapsed time: 22.979s

2) Detect architectural stripes

This is the core of the analysis and may take several minutes when processing large files.

user@dev:/tmp$ stripepy call 4DNFI9GMP2J8.mcool 10000

2025-01-14 12:48:25.002788 [info     ] CONFIG:
{
  "constrain_heights": false,
  "contact_map": "4DNFI9GMP2J8.mcool",
  "force": false,
  "genomic_belt": 5000000,
  "glob_pers_min": 0.05,
  "loc_pers_min": 0.33,
  "loc_trend_min": 0.25,
  "log_file": null,
  "max_width": 100000,
  "min_chrom_size": 2000000,
  "normalization": null,
  "nproc": 1,
  "output_file": "/tmp/4DNFI9GMP2J8.10000.hdf5",
  "plot_dir": null,
  "resolution": 10000,
  "roi": null
}
2025-01-14 12:48:25.002898 [info     ] validating file "4DNFI9GMP2J8.mcool" (10000bp)...
2025-01-14 12:48:25.014988 [info     ] file "4DNFI9GMP2J8.mcool" successfully validated
2025-01-14 12:48:25.015062 [info     ] initializing result file "/tmp/4DNFI9GMP2J8.10000.hdf5"...
2025-01-14 12:48:25.037560 [info     ] [chr1 ] begin processing...
2025-01-14 12:48:25.997439 [info     ] [chr1 ] [step 1    ] data pre-processing
2025-01-14 12:48:25.997584 [info     ] [chr1 ] [step 1.1  ] applying log-transformation
2025-01-14 12:48:26.041711 [info     ] [chr1 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:48:26.394097 [info     ] [chr1 ] [step 1.2  ] removed 49.92% of the non-zero entries (6800532/13623789)
2025-01-14 12:48:26.394249 [info     ] [chr1 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:48:26.470185 [info     ] [chr1 ] [step 1    ] preprocessing took 472.584ms
2025-01-14 12:48:26.470329 [info     ] [chr1 ] [step 2    ] topological data analysis
2025-01-14 12:48:26.470387 [info     ] [chr1 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:48:26.525759 [info     ] [chr1 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:48:26.525844 [info     ] [chr1 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:48:26.640500 [info     ] [chr1 ] [step 2.2.1] lower triangular part
2025-01-14 12:48:26.683243 [info     ] [chr1 ] [step 2.2.2] upper triangular part
2025-01-14 12:48:26.728946 [info     ] [chr1 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:48:26.858761 [info     ] [chr1 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1353 to 1304
2025-01-14 12:48:26.858891 [info     ] [chr1 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1217 to 1180
2025-01-14 12:48:26.858957 [info     ] [chr1 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:48:26.859452 [info     ] [chr1 ] [step 2.3.1] lower-triangular part: generated 1304 candidate stripes
2025-01-14 12:48:26.859562 [info     ] [chr1 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:48:26.860144 [info     ] [chr1 ] [step 2.3.2] upper-triangular part: generated 1180 candidate stripes
2025-01-14 12:48:26.860964 [info     ] [chr1 ] [step 2    ] topological data analysis took 390.586ms
2025-01-14 12:48:26.861002 [info     ] [chr1 ] [step 3    ] shape analysis
...
2025-01-14 12:50:13.141699 [info     ] [chrY ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:13.155257 [info     ] [chrY ] processing took 442.386ms
2025-01-14 12:50:13.155714 [info     ] DONE!
2025-01-14 12:50:13.155781 [info     ] processed 24 chromosomes in 1m:48.153s

Complete log

2025-01-14 12:48:25.002788 [info     ] CONFIG:
{
  "constrain_heights": false,
  "contact_map": "4DNFI9GMP2J8.mcool",
  "force": false,
  "genomic_belt": 5000000,
  "glob_pers_min": 0.05,
  "loc_pers_min": 0.33,
  "loc_trend_min": 0.25,
  "log_file": null,
  "max_width": 100000,
  "min_chrom_size": 2000000,
  "normalization": null,
  "nproc": 1,
  "output_file": "/tmp/4DNFI9GMP2J8.10000.hdf5",
  "plot_dir": null,
  "resolution": 10000,
  "roi": null
}
2025-01-14 12:48:25.002898 [info     ] validating file "4DNFI9GMP2J8.mcool" (10000bp)...
2025-01-14 12:48:25.014988 [info     ] file "4DNFI9GMP2J8.mcool" successfully validated
2025-01-14 12:48:25.015062 [info     ] initializing result file "/tmp/4DNFI9GMP2J8.10000.hdf5"...
2025-01-14 12:48:25.037560 [info     ] [chr1 ] begin processing...
2025-01-14 12:48:25.997439 [info     ] [chr1 ] [step 1    ] data pre-processing
2025-01-14 12:48:25.997584 [info     ] [chr1 ] [step 1.1  ] applying log-transformation
2025-01-14 12:48:26.041711 [info     ] [chr1 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:48:26.394097 [info     ] [chr1 ] [step 1.2  ] removed 49.92% of the non-zero entries (6800532/13623789)
2025-01-14 12:48:26.394249 [info     ] [chr1 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:48:26.470185 [info     ] [chr1 ] [step 1    ] preprocessing took 472.584ms
2025-01-14 12:48:26.470329 [info     ] [chr1 ] [step 2    ] topological data analysis
2025-01-14 12:48:26.470387 [info     ] [chr1 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:48:26.525759 [info     ] [chr1 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:48:26.525844 [info     ] [chr1 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:48:26.640500 [info     ] [chr1 ] [step 2.2.1] lower triangular part
2025-01-14 12:48:26.683243 [info     ] [chr1 ] [step 2.2.2] upper triangular part
2025-01-14 12:48:26.728946 [info     ] [chr1 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:48:26.858761 [info     ] [chr1 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1353 to 1304
2025-01-14 12:48:26.858891 [info     ] [chr1 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1217 to 1180
2025-01-14 12:48:26.858957 [info     ] [chr1 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:48:26.859452 [info     ] [chr1 ] [step 2.3.1] lower-triangular part: generated 1304 candidate stripes
2025-01-14 12:48:26.859562 [info     ] [chr1 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:48:26.860144 [info     ] [chr1 ] [step 2.3.2] upper-triangular part: generated 1180 candidate stripes
2025-01-14 12:48:26.860964 [info     ] [chr1 ] [step 2    ] topological data analysis took 390.586ms
2025-01-14 12:48:26.861002 [info     ] [chr1 ] [step 3    ] shape analysis
2025-01-14 12:48:26.861038 [info     ] [chr1 ] [step 3.1  ] width estimation
2025-01-14 12:48:26.861065 [info     ] [chr1 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:48:30.230277 [info     ] [chr1 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:48:30.230743 [info     ] [chr1 ] [step 3.1  ] width estimation took 3.370s
2025-01-14 12:48:30.230793 [info     ] [chr1 ] [step 3.2  ] height estimation
2025-01-14 12:48:30.230826 [info     ] [chr1 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:48:33.838096 [info     ] [chr1 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:48:33.838772 [info     ] [chr1 ] [step 3.2  ] height estimation took 3.608s
2025-01-14 12:48:33.838969 [info     ] [chr1 ] [step 3    ] shape analysis took 6.978s
2025-01-14 12:48:33.839010 [info     ] [chr1 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:48:33.839042 [info     ] [chr1 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:48:34.819194 [info     ] [chr1 ] [step 4    ] statistical analysis and post-processing took 980.140ms
2025-01-14 12:48:34.819317 [info     ] [chr1 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:48:34.871799 [info     ] [chr1 ] processing took 9.834s
2025-01-14 12:48:34.872016 [info     ] [chr2 ] begin processing...
2025-01-14 12:48:35.773199 [info     ] [chr2 ] [step 1    ] data pre-processing
2025-01-14 12:48:35.773344 [info     ] [chr2 ] [step 1.1  ] applying log-transformation
2025-01-14 12:48:35.817056 [info     ] [chr2 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:48:36.177891 [info     ] [chr2 ] [step 1.2  ] removed 49.92% of the non-zero entries (7159053/14341951)
2025-01-14 12:48:36.178036 [info     ] [chr2 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:48:36.264186 [info     ] [chr2 ] [step 1    ] preprocessing took 490.826ms
2025-01-14 12:48:36.264329 [info     ] [chr2 ] [step 2    ] topological data analysis
2025-01-14 12:48:36.264380 [info     ] [chr2 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:48:36.319916 [info     ] [chr2 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:48:36.320006 [info     ] [chr2 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:48:36.416495 [info     ] [chr2 ] [step 2.2.1] lower triangular part
2025-01-14 12:48:36.460423 [info     ] [chr2 ] [step 2.2.2] upper triangular part
2025-01-14 12:48:36.507180 [info     ] [chr2 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:48:36.647683 [info     ] [chr2 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1504 to 1473
2025-01-14 12:48:36.647747 [info     ] [chr2 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1402 to 1367
2025-01-14 12:48:36.647802 [info     ] [chr2 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:48:36.648376 [info     ] [chr2 ] [step 2.3.1] lower-triangular part: generated 1473 candidate stripes
2025-01-14 12:48:36.648508 [info     ] [chr2 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:48:36.649197 [info     ] [chr2 ] [step 2.3.2] upper-triangular part: generated 1367 candidate stripes
2025-01-14 12:48:36.650219 [info     ] [chr2 ] [step 2    ] topological data analysis took 385.850ms
2025-01-14 12:48:36.650327 [info     ] [chr2 ] [step 3    ] shape analysis
2025-01-14 12:48:36.650362 [info     ] [chr2 ] [step 3.1  ] width estimation
2025-01-14 12:48:36.650387 [info     ] [chr2 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:48:40.299274 [info     ] [chr2 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:48:40.300210 [info     ] [chr2 ] [step 3.1  ] width estimation took 3.650s
2025-01-14 12:48:40.300254 [info     ] [chr2 ] [step 3.2  ] height estimation
2025-01-14 12:48:40.300283 [info     ] [chr2 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:48:44.301992 [info     ] [chr2 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:48:44.302758 [info     ] [chr2 ] [step 3.2  ] height estimation took 4.002s
2025-01-14 12:48:44.303001 [info     ] [chr2 ] [step 3    ] shape analysis took 7.653s
2025-01-14 12:48:44.303044 [info     ] [chr2 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:48:44.303077 [info     ] [chr2 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:48:45.425307 [info     ] [chr2 ] [step 4    ] statistical analysis and post-processing took 1.122s
2025-01-14 12:48:45.425429 [info     ] [chr2 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:48:45.483981 [info     ] [chr2 ] processing took 10.612s
2025-01-14 12:48:45.484180 [info     ] [chr3 ] begin processing...
2025-01-14 12:48:46.206077 [info     ] [chr3 ] [step 1    ] data pre-processing
2025-01-14 12:48:46.206225 [info     ] [chr3 ] [step 1.1  ] applying log-transformation
2025-01-14 12:48:46.239501 [info     ] [chr3 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:48:46.516739 [info     ] [chr3 ] [step 1.2  ] removed 49.92% of the non-zero entries (5946460/11912543)
2025-01-14 12:48:46.516891 [info     ] [chr3 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:48:46.578467 [info     ] [chr3 ] [step 1    ] preprocessing took 372.222ms
2025-01-14 12:48:46.578615 [info     ] [chr3 ] [step 2    ] topological data analysis
2025-01-14 12:48:46.578665 [info     ] [chr3 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:48:46.623722 [info     ] [chr3 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:48:46.623815 [info     ] [chr3 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:48:46.703393 [info     ] [chr3 ] [step 2.2.1] lower triangular part
2025-01-14 12:48:46.739557 [info     ] [chr3 ] [step 2.2.2] upper triangular part
2025-01-14 12:48:46.778620 [info     ] [chr3 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:48:46.894006 [info     ] [chr3 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1173 to 1168
2025-01-14 12:48:46.894066 [info     ] [chr3 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1305 to 1297
2025-01-14 12:48:46.894125 [info     ] [chr3 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:48:46.894590 [info     ] [chr3 ] [step 2.3.1] lower-triangular part: generated 1168 candidate stripes
2025-01-14 12:48:46.894701 [info     ] [chr3 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:48:46.895343 [info     ] [chr3 ] [step 2.3.2] upper-triangular part: generated 1297 candidate stripes
2025-01-14 12:48:46.896215 [info     ] [chr3 ] [step 2    ] topological data analysis took 317.560ms
2025-01-14 12:48:46.896330 [info     ] [chr3 ] [step 3    ] shape analysis
2025-01-14 12:48:46.896362 [info     ] [chr3 ] [step 3.1  ] width estimation
2025-01-14 12:48:46.896388 [info     ] [chr3 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:48:49.704610 [info     ] [chr3 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:48:49.705369 [info     ] [chr3 ] [step 3.1  ] width estimation took 2.809s
2025-01-14 12:48:49.705471 [info     ] [chr3 ] [step 3.2  ] height estimation
2025-01-14 12:48:49.705534 [info     ] [chr3 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:48:53.106184 [info     ] [chr3 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:48:53.106866 [info     ] [chr3 ] [step 3.2  ] height estimation took 3.401s
2025-01-14 12:48:53.107150 [info     ] [chr3 ] [step 3    ] shape analysis took 6.211s
2025-01-14 12:48:53.107201 [info     ] [chr3 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:48:53.107236 [info     ] [chr3 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:48:53.995859 [info     ] [chr3 ] [step 4    ] statistical analysis and post-processing took 888.608ms
2025-01-14 12:48:53.995982 [info     ] [chr3 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:48:54.043330 [info     ] [chr3 ] processing took 8.559s
2025-01-14 12:48:54.043530 [info     ] [chr4 ] begin processing...
2025-01-14 12:48:54.615181 [info     ] [chr4 ] [step 1    ] data pre-processing
2025-01-14 12:48:54.615321 [info     ] [chr4 ] [step 1.1  ] applying log-transformation
2025-01-14 12:48:54.638890 [info     ] [chr4 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:48:54.902263 [info     ] [chr4 ] [step 1.2  ] removed 49.91% of the non-zero entries (5473149/10965107)
2025-01-14 12:48:54.902426 [info     ] [chr4 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:48:54.968124 [info     ] [chr4 ] [step 1    ] preprocessing took 352.783ms
2025-01-14 12:48:54.968275 [info     ] [chr4 ] [step 2    ] topological data analysis
2025-01-14 12:48:54.968324 [info     ] [chr4 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:48:55.006404 [info     ] [chr4 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:48:55.006532 [info     ] [chr4 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:48:55.101248 [info     ] [chr4 ] [step 2.2.1] lower triangular part
2025-01-14 12:48:55.132420 [info     ] [chr4 ] [step 2.2.2] upper triangular part
2025-01-14 12:48:55.165599 [info     ] [chr4 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:48:55.263648 [info     ] [chr4 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1152 to 1144
2025-01-14 12:48:55.263770 [info     ] [chr4 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 993 to 985
2025-01-14 12:48:55.263828 [info     ] [chr4 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:48:55.264248 [info     ] [chr4 ] [step 2.3.1] lower-triangular part: generated 1144 candidate stripes
2025-01-14 12:48:55.264356 [info     ] [chr4 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:48:55.264845 [info     ] [chr4 ] [step 2.3.2] upper-triangular part: generated 985 candidate stripes
2025-01-14 12:48:55.265838 [info     ] [chr4 ] [step 2    ] topological data analysis took 297.524ms
2025-01-14 12:48:55.265962 [info     ] [chr4 ] [step 3    ] shape analysis
2025-01-14 12:48:55.265994 [info     ] [chr4 ] [step 3.1  ] width estimation
2025-01-14 12:48:55.266017 [info     ] [chr4 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:48:57.293326 [info     ] [chr4 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:48:57.293895 [info     ] [chr4 ] [step 3.1  ] width estimation took 2.028s
2025-01-14 12:48:57.293959 [info     ] [chr4 ] [step 3.2  ] height estimation
2025-01-14 12:48:57.293999 [info     ] [chr4 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:48:59.921469 [info     ] [chr4 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:48:59.922046 [info     ] [chr4 ] [step 3.2  ] height estimation took 2.628s
2025-01-14 12:48:59.922325 [info     ] [chr4 ] [step 3    ] shape analysis took 4.656s
2025-01-14 12:48:59.922370 [info     ] [chr4 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:48:59.922397 [info     ] [chr4 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:00.635691 [info     ] [chr4 ] [step 4    ] statistical analysis and post-processing took 713.281ms
2025-01-14 12:49:00.635819 [info     ] [chr4 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:00.678109 [info     ] [chr4 ] processing took 6.635s
2025-01-14 12:49:00.678311 [info     ] [chr5 ] begin processing...
2025-01-14 12:49:01.232136 [info     ] [chr5 ] [step 1    ] data pre-processing
2025-01-14 12:49:01.232285 [info     ] [chr5 ] [step 1.1  ] applying log-transformation
2025-01-14 12:49:01.252853 [info     ] [chr5 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:01.500614 [info     ] [chr5 ] [step 1.2  ] removed 49.92% of the non-zero entries (5281978/10581676)
2025-01-14 12:49:01.500778 [info     ] [chr5 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:01.560841 [info     ] [chr5 ] [step 1    ] preprocessing took 328.538ms
2025-01-14 12:49:01.560990 [info     ] [chr5 ] [step 2    ] topological data analysis
2025-01-14 12:49:01.561041 [info     ] [chr5 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:01.598494 [info     ] [chr5 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:01.598625 [info     ] [chr5 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:01.665965 [info     ] [chr5 ] [step 2.2.1] lower triangular part
2025-01-14 12:49:01.696991 [info     ] [chr5 ] [step 2.2.2] upper triangular part
2025-01-14 12:49:01.729874 [info     ] [chr5 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:01.825891 [info     ] [chr5 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 978 to 967
2025-01-14 12:49:01.825997 [info     ] [chr5 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1365 to 1353
2025-01-14 12:49:01.826052 [info     ] [chr5 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:01.826428 [info     ] [chr5 ] [step 2.3.1] lower-triangular part: generated 967 candidate stripes
2025-01-14 12:49:01.826515 [info     ] [chr5 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:01.827155 [info     ] [chr5 ] [step 2.3.2] upper-triangular part: generated 1353 candidate stripes
2025-01-14 12:49:01.828096 [info     ] [chr5 ] [step 2    ] topological data analysis took 267.065ms
2025-01-14 12:49:01.828214 [info     ] [chr5 ] [step 3    ] shape analysis
2025-01-14 12:49:01.828244 [info     ] [chr5 ] [step 3.1  ] width estimation
2025-01-14 12:49:01.828268 [info     ] [chr5 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:04.094841 [info     ] [chr5 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:04.095354 [info     ] [chr5 ] [step 3.1  ] width estimation took 2.267s
2025-01-14 12:49:04.095410 [info     ] [chr5 ] [step 3.2  ] height estimation
2025-01-14 12:49:04.095442 [info     ] [chr5 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:07.020664 [info     ] [chr5 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:07.021280 [info     ] [chr5 ] [step 3.2  ] height estimation took 2.926s
2025-01-14 12:49:07.021544 [info     ] [chr5 ] [step 3    ] shape analysis took 5.193s
2025-01-14 12:49:07.021582 [info     ] [chr5 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:07.021610 [info     ] [chr5 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:07.826098 [info     ] [chr5 ] [step 4    ] statistical analysis and post-processing took 804.473ms
2025-01-14 12:49:07.826219 [info     ] [chr5 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:07.870644 [info     ] [chr5 ] processing took 7.192s
2025-01-14 12:49:07.870840 [info     ] [chr6 ] begin processing...
2025-01-14 12:49:08.404902 [info     ] [chr6 ] [step 1    ] data pre-processing
2025-01-14 12:49:08.405044 [info     ] [chr6 ] [step 1.1  ] applying log-transformation
2025-01-14 12:49:08.423929 [info     ] [chr6 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:08.654928 [info     ] [chr6 ] [step 1.2  ] removed 49.92% of the non-zero entries (5062685/10142231)
2025-01-14 12:49:08.655083 [info     ] [chr6 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:08.708001 [info     ] [chr6 ] [step 1    ] preprocessing took 302.940ms
2025-01-14 12:49:08.708171 [info     ] [chr6 ] [step 2    ] topological data analysis
2025-01-14 12:49:08.708230 [info     ] [chr6 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:08.742292 [info     ] [chr6 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:08.742421 [info     ] [chr6 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:08.803504 [info     ] [chr6 ] [step 2.2.1] lower triangular part
2025-01-14 12:49:08.832908 [info     ] [chr6 ] [step 2.2.2] upper triangular part
2025-01-14 12:49:08.864552 [info     ] [chr6 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:08.954081 [info     ] [chr6 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1102 to 1087
2025-01-14 12:49:08.954147 [info     ] [chr6 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 986 to 975
2025-01-14 12:49:08.954199 [info     ] [chr6 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:08.954594 [info     ] [chr6 ] [step 2.3.1] lower-triangular part: generated 1087 candidate stripes
2025-01-14 12:49:08.954687 [info     ] [chr6 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:08.955185 [info     ] [chr6 ] [step 2.3.2] upper-triangular part: generated 975 candidate stripes
2025-01-14 12:49:08.956032 [info     ] [chr6 ] [step 2    ] topological data analysis took 247.812ms
2025-01-14 12:49:08.956158 [info     ] [chr6 ] [step 3    ] shape analysis
2025-01-14 12:49:08.956190 [info     ] [chr6 ] [step 3.1  ] width estimation
2025-01-14 12:49:08.956215 [info     ] [chr6 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:10.707434 [info     ] [chr6 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:10.707903 [info     ] [chr6 ] [step 3.1  ] width estimation took 1.752s
2025-01-14 12:49:10.707947 [info     ] [chr6 ] [step 3.2  ] height estimation
2025-01-14 12:49:10.707978 [info     ] [chr6 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:13.324728 [info     ] [chr6 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:13.325328 [info     ] [chr6 ] [step 3.2  ] height estimation took 2.617s
2025-01-14 12:49:13.325599 [info     ] [chr6 ] [step 3    ] shape analysis took 4.369s
2025-01-14 12:49:13.325638 [info     ] [chr6 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:13.325670 [info     ] [chr6 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:14.047510 [info     ] [chr6 ] [step 4    ] statistical analysis and post-processing took 721.825ms
2025-01-14 12:49:14.047652 [info     ] [chr6 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:14.090589 [info     ] [chr6 ] processing took 6.220s
2025-01-14 12:49:14.090785 [info     ] [chr7 ] begin processing...
2025-01-14 12:49:14.553816 [info     ] [chr7 ] [step 1    ] data pre-processing
2025-01-14 12:49:14.553956 [info     ] [chr7 ] [step 1.1  ] applying log-transformation
2025-01-14 12:49:14.571432 [info     ] [chr7 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:14.763864 [info     ] [chr7 ] [step 1.2  ] removed 49.91% of the non-zero entries (4510986/9037570)
2025-01-14 12:49:14.764019 [info     ] [chr7 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:14.806433 [info     ] [chr7 ] [step 1    ] preprocessing took 252.460ms
2025-01-14 12:49:14.806579 [info     ] [chr7 ] [step 2    ] topological data analysis
2025-01-14 12:49:14.806628 [info     ] [chr7 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:14.838401 [info     ] [chr7 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:14.838526 [info     ] [chr7 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:14.894711 [info     ] [chr7 ] [step 2.2.1] lower triangular part
2025-01-14 12:49:14.920210 [info     ] [chr7 ] [step 2.2.2] upper triangular part
2025-01-14 12:49:14.948121 [info     ] [chr7 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:15.029561 [info     ] [chr7 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 770 to 735
2025-01-14 12:49:15.029634 [info     ] [chr7 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1114 to 1083
2025-01-14 12:49:15.029688 [info     ] [chr7 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:15.029990 [info     ] [chr7 ] [step 2.3.1] lower-triangular part: generated 735 candidate stripes
2025-01-14 12:49:15.030062 [info     ] [chr7 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:15.030454 [info     ] [chr7 ] [step 2.3.2] upper-triangular part: generated 1083 candidate stripes
2025-01-14 12:49:15.031180 [info     ] [chr7 ] [step 2    ] topological data analysis took 224.563ms
2025-01-14 12:49:15.031288 [info     ] [chr7 ] [step 3    ] shape analysis
2025-01-14 12:49:15.031323 [info     ] [chr7 ] [step 3.1  ] width estimation
2025-01-14 12:49:15.031349 [info     ] [chr7 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:16.547349 [info     ] [chr7 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:16.547689 [info     ] [chr7 ] [step 3.1  ] width estimation took 1.516s
2025-01-14 12:49:16.547731 [info     ] [chr7 ] [step 3.2  ] height estimation
2025-01-14 12:49:16.547761 [info     ] [chr7 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:18.851984 [info     ] [chr7 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:18.852521 [info     ] [chr7 ] [step 3.2  ] height estimation took 2.305s
2025-01-14 12:49:18.852749 [info     ] [chr7 ] [step 3    ] shape analysis took 3.821s
2025-01-14 12:49:18.852790 [info     ] [chr7 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:18.852820 [info     ] [chr7 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:19.490033 [info     ] [chr7 ] [step 4    ] statistical analysis and post-processing took 637.199ms
2025-01-14 12:49:19.490164 [info     ] [chr7 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:19.529120 [info     ] [chr7 ] processing took 5.438s
2025-01-14 12:49:19.529310 [info     ] [chr8 ] begin processing...
2025-01-14 12:49:19.954370 [info     ] [chr8 ] [step 1    ] data pre-processing
2025-01-14 12:49:19.954511 [info     ] [chr8 ] [step 1.1  ] applying log-transformation
2025-01-14 12:49:19.970042 [info     ] [chr8 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:20.152033 [info     ] [chr8 ] [step 1.2  ] removed 49.92% of the non-zero entries (4272912/8560081)
2025-01-14 12:49:20.152184 [info     ] [chr8 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:20.191894 [info     ] [chr8 ] [step 1    ] preprocessing took 237.366ms
2025-01-14 12:49:20.192037 [info     ] [chr8 ] [step 2    ] topological data analysis
2025-01-14 12:49:20.192094 [info     ] [chr8 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:20.222810 [info     ] [chr8 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:20.222925 [info     ] [chr8 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:20.277482 [info     ] [chr8 ] [step 2.2.1] lower triangular part
2025-01-14 12:49:20.302332 [info     ] [chr8 ] [step 2.2.2] upper triangular part
2025-01-14 12:49:20.329843 [info     ] [chr8 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:20.408206 [info     ] [chr8 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 950 to 927
2025-01-14 12:49:20.408287 [info     ] [chr8 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 789 to 770
2025-01-14 12:49:20.408338 [info     ] [chr8 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:20.408698 [info     ] [chr8 ] [step 2.3.1] lower-triangular part: generated 927 candidate stripes
2025-01-14 12:49:20.408783 [info     ] [chr8 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:20.409079 [info     ] [chr8 ] [step 2.3.2] upper-triangular part: generated 770 candidate stripes
2025-01-14 12:49:20.409758 [info     ] [chr8 ] [step 2    ] topological data analysis took 217.683ms
2025-01-14 12:49:20.409864 [info     ] [chr8 ] [step 3    ] shape analysis
2025-01-14 12:49:20.409895 [info     ] [chr8 ] [step 3.1  ] width estimation
2025-01-14 12:49:20.409918 [info     ] [chr8 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:21.753341 [info     ] [chr8 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:21.753654 [info     ] [chr8 ] [step 3.1  ] width estimation took 1.344s
2025-01-14 12:49:21.753699 [info     ] [chr8 ] [step 3.2  ] height estimation
2025-01-14 12:49:21.753728 [info     ] [chr8 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:23.939159 [info     ] [chr8 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:23.939660 [info     ] [chr8 ] [step 3.2  ] height estimation took 2.186s
2025-01-14 12:49:23.939898 [info     ] [chr8 ] [step 3    ] shape analysis took 3.530s
2025-01-14 12:49:23.939938 [info     ] [chr8 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:23.939968 [info     ] [chr8 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:24.533027 [info     ] [chr8 ] [step 4    ] statistical analysis and post-processing took 593.046ms
2025-01-14 12:49:24.533155 [info     ] [chr8 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:24.569016 [info     ] [chr8 ] processing took 5.040s
2025-01-14 12:49:24.569208 [info     ] [chr9 ] begin processing...
2025-01-14 12:49:24.920078 [info     ] [chr9 ] [step 1    ] data pre-processing
2025-01-14 12:49:24.920234 [info     ] [chr9 ] [step 1.1  ] applying log-transformation
2025-01-14 12:49:24.933661 [info     ] [chr9 ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:25.064319 [info     ] [chr9 ] [step 1.2  ] removed 49.91% of the non-zero entries (3400203/6812131)
2025-01-14 12:49:25.064474 [info     ] [chr9 ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:25.089706 [info     ] [chr9 ] [step 1    ] preprocessing took 169.460ms
2025-01-14 12:49:25.089857 [info     ] [chr9 ] [step 2    ] topological data analysis
2025-01-14 12:49:25.089908 [info     ] [chr9 ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:25.117704 [info     ] [chr9 ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:25.117814 [info     ] [chr9 ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:25.167338 [info     ] [chr9 ] [step 2.2.1] lower triangular part
2025-01-14 12:49:25.189500 [info     ] [chr9 ] [step 2.2.2] upper triangular part
2025-01-14 12:49:25.213548 [info     ] [chr9 ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:25.283661 [info     ] [chr9 ] [step 2.2.3] lower triangular part: number of seed sites reduced from 602 to 587
2025-01-14 12:49:25.283756 [info     ] [chr9 ] [step 2.2.3] upper triangular part: number of seed sites reduced from 690 to 675
2025-01-14 12:49:25.283811 [info     ] [chr9 ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:25.284065 [info     ] [chr9 ] [step 2.3.1] lower-triangular part: generated 587 candidate stripes
2025-01-14 12:49:25.284141 [info     ] [chr9 ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:25.284401 [info     ] [chr9 ] [step 2.3.2] upper-triangular part: generated 675 candidate stripes
2025-01-14 12:49:25.285081 [info     ] [chr9 ] [step 2    ] topological data analysis took 195.178ms
2025-01-14 12:49:25.285192 [info     ] [chr9 ] [step 3    ] shape analysis
2025-01-14 12:49:25.285224 [info     ] [chr9 ] [step 3.1  ] width estimation
2025-01-14 12:49:25.285249 [info     ] [chr9 ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:26.243649 [info     ] [chr9 ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:26.244027 [info     ] [chr9 ] [step 3.1  ] width estimation took 958.796ms
2025-01-14 12:49:26.244083 [info     ] [chr9 ] [step 3.2  ] height estimation
2025-01-14 12:49:26.244115 [info     ] [chr9 ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:27.905512 [info     ] [chr9 ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:27.905968 [info     ] [chr9 ] [step 3.2  ] height estimation took 1.662s
2025-01-14 12:49:27.906195 [info     ] [chr9 ] [step 3    ] shape analysis took 2.621s
2025-01-14 12:49:27.906237 [info     ] [chr9 ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:27.906266 [info     ] [chr9 ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:28.371493 [info     ] [chr9 ] [step 4    ] statistical analysis and post-processing took 465.213ms
2025-01-14 12:49:28.371618 [info     ] [chr9 ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:28.402213 [info     ] [chr9 ] processing took 3.833s
2025-01-14 12:49:28.402398 [info     ] [chr10] begin processing...
2025-01-14 12:49:28.812231 [info     ] [chr10] [step 1    ] data pre-processing
2025-01-14 12:49:28.812375 [info     ] [chr10] [step 1.1  ] applying log-transformation
2025-01-14 12:49:28.827574 [info     ] [chr10] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:28.984694 [info     ] [chr10] [step 1.2  ] removed 49.92% of the non-zero entries (4024072/8061306)
2025-01-14 12:49:28.984838 [info     ] [chr10] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:29.017076 [info     ] [chr10] [step 1    ] preprocessing took 204.684ms
2025-01-14 12:49:29.017223 [info     ] [chr10] [step 2    ] topological data analysis
2025-01-14 12:49:29.017271 [info     ] [chr10] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:29.044196 [info     ] [chr10] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:29.044313 [info     ] [chr10] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:29.091342 [info     ] [chr10] [step 2.2.1] lower triangular part
2025-01-14 12:49:29.112882 [info     ] [chr10] [step 2.2.2] upper triangular part
2025-01-14 12:49:29.136692 [info     ] [chr10] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:29.205133 [info     ] [chr10] [step 2.2.3] lower triangular part: number of seed sites reduced from 855 to 830
2025-01-14 12:49:29.205196 [info     ] [chr10] [step 2.2.3] upper triangular part: number of seed sites reduced from 891 to 867
2025-01-14 12:49:29.205246 [info     ] [chr10] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:29.205557 [info     ] [chr10] [step 2.3.1] lower-triangular part: generated 830 candidate stripes
2025-01-14 12:49:29.205636 [info     ] [chr10] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:29.205948 [info     ] [chr10] [step 2.3.2] upper-triangular part: generated 867 candidate stripes
2025-01-14 12:49:29.206482 [info     ] [chr10] [step 2    ] topological data analysis took 189.221ms
2025-01-14 12:49:29.206566 [info     ] [chr10] [step 3    ] shape analysis
2025-01-14 12:49:29.206596 [info     ] [chr10] [step 3.1  ] width estimation
2025-01-14 12:49:29.206619 [info     ] [chr10] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:30.437109 [info     ] [chr10] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:30.437479 [info     ] [chr10] [step 3.1  ] width estimation took 1.231s
2025-01-14 12:49:30.437524 [info     ] [chr10] [step 3.2  ] height estimation
2025-01-14 12:49:30.437556 [info     ] [chr10] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:32.882541 [info     ] [chr10] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:32.883045 [info     ] [chr10] [step 3.2  ] height estimation took 2.445s
2025-01-14 12:49:32.883249 [info     ] [chr10] [step 3    ] shape analysis took 3.677s
2025-01-14 12:49:32.883292 [info     ] [chr10] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:32.883323 [info     ] [chr10] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:33.560662 [info     ] [chr10] [step 4    ] statistical analysis and post-processing took 677.325ms
2025-01-14 12:49:33.560787 [info     ] [chr10] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:33.599771 [info     ] [chr10] processing took 5.197s
2025-01-14 12:49:33.599965 [info     ] [chr11] begin processing...
2025-01-14 12:49:34.032197 [info     ] [chr11] [step 1    ] data pre-processing
2025-01-14 12:49:34.032325 [info     ] [chr11] [step 1.1  ] applying log-transformation
2025-01-14 12:49:34.047121 [info     ] [chr11] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:34.197151 [info     ] [chr11] [step 1.2  ] removed 49.92% of the non-zero entries (4016918/8046984)
2025-01-14 12:49:34.197302 [info     ] [chr11] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:34.228773 [info     ] [chr11] [step 1    ] preprocessing took 196.429ms
2025-01-14 12:49:34.228925 [info     ] [chr11] [step 2    ] topological data analysis
2025-01-14 12:49:34.228971 [info     ] [chr11] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:34.255824 [info     ] [chr11] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:34.255902 [info     ] [chr11] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:34.305550 [info     ] [chr11] [step 2.2.1] lower triangular part
2025-01-14 12:49:34.328177 [info     ] [chr11] [step 2.2.2] upper triangular part
2025-01-14 12:49:34.353140 [info     ] [chr11] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:34.423134 [info     ] [chr11] [step 2.2.3] lower triangular part: number of seed sites reduced from 909 to 897
2025-01-14 12:49:34.423196 [info     ] [chr11] [step 2.2.3] upper triangular part: number of seed sites reduced from 1056 to 1044
2025-01-14 12:49:34.423246 [info     ] [chr11] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:34.423851 [info     ] [chr11] [step 2.3.1] lower-triangular part: generated 897 candidate stripes
2025-01-14 12:49:34.423994 [info     ] [chr11] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:34.424499 [info     ] [chr11] [step 2.3.2] upper-triangular part: generated 1044 candidate stripes
2025-01-14 12:49:34.425238 [info     ] [chr11] [step 2    ] topological data analysis took 196.276ms
2025-01-14 12:49:34.425343 [info     ] [chr11] [step 3    ] shape analysis
2025-01-14 12:49:34.425379 [info     ] [chr11] [step 3.1  ] width estimation
2025-01-14 12:49:34.425404 [info     ] [chr11] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:35.732201 [info     ] [chr11] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:35.732588 [info     ] [chr11] [step 3.1  ] width estimation took 1.307s
2025-01-14 12:49:35.732639 [info     ] [chr11] [step 3.2  ] height estimation
2025-01-14 12:49:35.732669 [info     ] [chr11] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:38.152223 [info     ] [chr11] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:38.152767 [info     ] [chr11] [step 3.2  ] height estimation took 2.420s
2025-01-14 12:49:38.153063 [info     ] [chr11] [step 3    ] shape analysis took 3.728s
2025-01-14 12:49:38.153108 [info     ] [chr11] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:38.153137 [info     ] [chr11] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:38.810454 [info     ] [chr11] [step 4    ] statistical analysis and post-processing took 657.304ms
2025-01-14 12:49:38.810577 [info     ] [chr11] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:38.850110 [info     ] [chr11] processing took 5.250s
2025-01-14 12:49:38.850313 [info     ] [chr12] begin processing...
2025-01-14 12:49:39.227504 [info     ] [chr12] [step 1    ] data pre-processing
2025-01-14 12:49:39.227642 [info     ] [chr12] [step 1.1  ] applying log-transformation
2025-01-14 12:49:39.242849 [info     ] [chr12] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:39.389986 [info     ] [chr12] [step 1.2  ] removed 49.92% of the non-zero entries (3923466/7860067)
2025-01-14 12:49:39.390145 [info     ] [chr12] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:39.423179 [info     ] [chr12] [step 1    ] preprocessing took 195.517ms
2025-01-14 12:49:39.423330 [info     ] [chr12] [step 2    ] topological data analysis
2025-01-14 12:49:39.423380 [info     ] [chr12] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:39.451041 [info     ] [chr12] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:39.451167 [info     ] [chr12] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:39.500378 [info     ] [chr12] [step 2.2.1] lower triangular part
2025-01-14 12:49:39.522845 [info     ] [chr12] [step 2.2.2] upper triangular part
2025-01-14 12:49:39.547803 [info     ] [chr12] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:39.618224 [info     ] [chr12] [step 2.2.3] lower triangular part: number of seed sites reduced from 633 to 629
2025-01-14 12:49:39.618291 [info     ] [chr12] [step 2.2.3] upper triangular part: number of seed sites reduced from 883 to 878
2025-01-14 12:49:39.618339 [info     ] [chr12] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:39.618605 [info     ] [chr12] [step 2.3.1] lower-triangular part: generated 629 candidate stripes
2025-01-14 12:49:39.618672 [info     ] [chr12] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:39.619003 [info     ] [chr12] [step 2.3.2] upper-triangular part: generated 878 candidate stripes
2025-01-14 12:49:39.619669 [info     ] [chr12] [step 2    ] topological data analysis took 196.301ms
2025-01-14 12:49:39.619780 [info     ] [chr12] [step 3    ] shape analysis
2025-01-14 12:49:39.619810 [info     ] [chr12] [step 3.1  ] width estimation
2025-01-14 12:49:39.619833 [info     ] [chr12] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:40.733611 [info     ] [chr12] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:40.733916 [info     ] [chr12] [step 3.1  ] width estimation took 1.114s
2025-01-14 12:49:40.733965 [info     ] [chr12] [step 3.2  ] height estimation
2025-01-14 12:49:40.733995 [info     ] [chr12] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:42.638918 [info     ] [chr12] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:42.639391 [info     ] [chr12] [step 3.2  ] height estimation took 1.905s
2025-01-14 12:49:42.639642 [info     ] [chr12] [step 3    ] shape analysis took 3.020s
2025-01-14 12:49:42.639683 [info     ] [chr12] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:42.639712 [info     ] [chr12] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:43.147454 [info     ] [chr12] [step 4    ] statistical analysis and post-processing took 507.727ms
2025-01-14 12:49:43.147582 [info     ] [chr12] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:43.180693 [info     ] [chr12] processing took 4.330s
2025-01-14 12:49:43.180900 [info     ] [chr13] begin processing...
2025-01-14 12:49:43.465271 [info     ] [chr13] [step 1    ] data pre-processing
2025-01-14 12:49:43.465418 [info     ] [chr13] [step 1.1  ] applying log-transformation
2025-01-14 12:49:43.476459 [info     ] [chr13] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:43.581261 [info     ] [chr13] [step 1.2  ] removed 49.91% of the non-zero entries (2835198/5680101)
2025-01-14 12:49:43.581409 [info     ] [chr13] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:43.604671 [info     ] [chr13] [step 1    ] preprocessing took 139.236ms
2025-01-14 12:49:43.604820 [info     ] [chr13] [step 2    ] topological data analysis
2025-01-14 12:49:43.604868 [info     ] [chr13] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:43.626394 [info     ] [chr13] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:43.626496 [info     ] [chr13] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:43.686825 [info     ] [chr13] [step 2.2.1] lower triangular part
2025-01-14 12:49:43.704543 [info     ] [chr13] [step 2.2.2] upper triangular part
2025-01-14 12:49:43.724168 [info     ] [chr13] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:43.781743 [info     ] [chr13] [step 2.2.3] lower triangular part: number of seed sites reduced from 686 to 675
2025-01-14 12:49:43.781856 [info     ] [chr13] [step 2.2.3] upper triangular part: number of seed sites reduced from 653 to 643
2025-01-14 12:49:43.781916 [info     ] [chr13] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:43.782217 [info     ] [chr13] [step 2.3.1] lower-triangular part: generated 675 candidate stripes
2025-01-14 12:49:43.782291 [info     ] [chr13] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:43.782548 [info     ] [chr13] [step 2.3.2] upper-triangular part: generated 643 candidate stripes
2025-01-14 12:49:43.783274 [info     ] [chr13] [step 2    ] topological data analysis took 178.417ms
2025-01-14 12:49:43.783373 [info     ] [chr13] [step 3    ] shape analysis
2025-01-14 12:49:43.783405 [info     ] [chr13] [step 3.1  ] width estimation
2025-01-14 12:49:43.783429 [info     ] [chr13] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:44.624260 [info     ] [chr13] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:44.624471 [info     ] [chr13] [step 3.1  ] width estimation took 841.062ms
2025-01-14 12:49:44.624509 [info     ] [chr13] [step 3.2  ] height estimation
2025-01-14 12:49:44.624538 [info     ] [chr13] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:46.262463 [info     ] [chr13] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:46.262915 [info     ] [chr13] [step 3.2  ] height estimation took 1.638s
2025-01-14 12:49:46.263148 [info     ] [chr13] [step 3    ] shape analysis took 2.480s
2025-01-14 12:49:46.263200 [info     ] [chr13] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:46.263233 [info     ] [chr13] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:46.704847 [info     ] [chr13] [step 4    ] statistical analysis and post-processing took 441.600ms
2025-01-14 12:49:46.704975 [info     ] [chr13] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:46.736772 [info     ] [chr13] processing took 3.556s
2025-01-14 12:49:46.736966 [info     ] [chr14] begin processing...
2025-01-14 12:49:47.004331 [info     ] [chr14] [step 1    ] data pre-processing
2025-01-14 12:49:47.004466 [info     ] [chr14] [step 1.1  ] applying log-transformation
2025-01-14 12:49:47.014943 [info     ] [chr14] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:47.113898 [info     ] [chr14] [step 1.2  ] removed 49.92% of the non-zero entries (2640852/5290549)
2025-01-14 12:49:47.114041 [info     ] [chr14] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:47.135676 [info     ] [chr14] [step 1    ] preprocessing took 131.193ms
2025-01-14 12:49:47.135823 [info     ] [chr14] [step 2    ] topological data analysis
2025-01-14 12:49:47.135872 [info     ] [chr14] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:47.155339 [info     ] [chr14] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:47.155431 [info     ] [chr14] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:47.190277 [info     ] [chr14] [step 2.2.1] lower triangular part
2025-01-14 12:49:47.206234 [info     ] [chr14] [step 2.2.2] upper triangular part
2025-01-14 12:49:47.224185 [info     ] [chr14] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:47.278803 [info     ] [chr14] [step 2.2.3] lower triangular part: number of seed sites reduced from 567 to 561
2025-01-14 12:49:47.278863 [info     ] [chr14] [step 2.2.3] upper triangular part: number of seed sites reduced from 523 to 521
2025-01-14 12:49:47.278913 [info     ] [chr14] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:47.279165 [info     ] [chr14] [step 2.3.1] lower-triangular part: generated 561 candidate stripes
2025-01-14 12:49:47.279230 [info     ] [chr14] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:47.279438 [info     ] [chr14] [step 2.3.2] upper-triangular part: generated 521 candidate stripes
2025-01-14 12:49:47.279905 [info     ] [chr14] [step 2    ] topological data analysis took 144.044ms
2025-01-14 12:49:47.279989 [info     ] [chr14] [step 3    ] shape analysis
2025-01-14 12:49:47.280019 [info     ] [chr14] [step 3.1  ] width estimation
2025-01-14 12:49:47.280043 [info     ] [chr14] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:47.929314 [info     ] [chr14] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:47.929537 [info     ] [chr14] [step 3.1  ] width estimation took 649.514ms
2025-01-14 12:49:47.929583 [info     ] [chr14] [step 3.2  ] height estimation
2025-01-14 12:49:47.929612 [info     ] [chr14] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:49.314962 [info     ] [chr14] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:49.315342 [info     ] [chr14] [step 3.2  ] height estimation took 1.386s
2025-01-14 12:49:49.315521 [info     ] [chr14] [step 3    ] shape analysis took 2.036s
2025-01-14 12:49:49.315565 [info     ] [chr14] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:49.315593 [info     ] [chr14] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:49.688815 [info     ] [chr14] [step 4    ] statistical analysis and post-processing took 373.208ms
2025-01-14 12:49:49.688943 [info     ] [chr14] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:49.716808 [info     ] [chr14] processing took 2.980s
2025-01-14 12:49:49.717017 [info     ] [chr15] begin processing...
2025-01-14 12:49:49.956410 [info     ] [chr15] [step 1    ] data pre-processing
2025-01-14 12:49:49.956558 [info     ] [chr15] [step 1.1  ] applying log-transformation
2025-01-14 12:49:49.966169 [info     ] [chr15] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:50.057111 [info     ] [chr15] [step 1.2  ] removed 49.91% of the non-zero entries (2375894/4759909)
2025-01-14 12:49:50.057269 [info     ] [chr15] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:50.074474 [info     ] [chr15] [step 1    ] preprocessing took 117.900ms
2025-01-14 12:49:50.074632 [info     ] [chr15] [step 2    ] topological data analysis
2025-01-14 12:49:50.074683 [info     ] [chr15] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:50.093699 [info     ] [chr15] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:50.093792 [info     ] [chr15] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:50.128269 [info     ] [chr15] [step 2.2.1] lower triangular part
2025-01-14 12:49:50.144259 [info     ] [chr15] [step 2.2.2] upper triangular part
2025-01-14 12:49:50.162169 [info     ] [chr15] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:50.212507 [info     ] [chr15] [step 2.2.3] lower triangular part: number of seed sites reduced from 637 to 602
2025-01-14 12:49:50.212566 [info     ] [chr15] [step 2.2.3] upper triangular part: number of seed sites reduced from 635 to 607
2025-01-14 12:49:50.212615 [info     ] [chr15] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:50.212883 [info     ] [chr15] [step 2.3.1] lower-triangular part: generated 602 candidate stripes
2025-01-14 12:49:50.212953 [info     ] [chr15] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:50.213200 [info     ] [chr15] [step 2.3.2] upper-triangular part: generated 607 candidate stripes
2025-01-14 12:49:50.213617 [info     ] [chr15] [step 2    ] topological data analysis took 138.946ms
2025-01-14 12:49:50.213695 [info     ] [chr15] [step 3    ] shape analysis
2025-01-14 12:49:50.213723 [info     ] [chr15] [step 3.1  ] width estimation
2025-01-14 12:49:50.213745 [info     ] [chr15] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:50.890529 [info     ] [chr15] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:50.890811 [info     ] [chr15] [step 3.1  ] width estimation took 677.083ms
2025-01-14 12:49:50.890855 [info     ] [chr15] [step 3.2  ] height estimation
2025-01-14 12:49:50.890886 [info     ] [chr15] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:52.377000 [info     ] [chr15] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:52.377407 [info     ] [chr15] [step 3.2  ] height estimation took 1.487s
2025-01-14 12:49:52.377609 [info     ] [chr15] [step 3    ] shape analysis took 2.164s
2025-01-14 12:49:52.377648 [info     ] [chr15] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:52.377679 [info     ] [chr15] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:52.778180 [info     ] [chr15] [step 4    ] statistical analysis and post-processing took 400.486ms
2025-01-14 12:49:52.778300 [info     ] [chr15] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:52.806234 [info     ] [chr15] processing took 3.089s
2025-01-14 12:49:52.806421 [info     ] [chr16] begin processing...
2025-01-14 12:49:53.034117 [info     ] [chr16] [step 1    ] data pre-processing
2025-01-14 12:49:53.034262 [info     ] [chr16] [step 1.1  ] applying log-transformation
2025-01-14 12:49:53.043151 [info     ] [chr16] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:53.136870 [info     ] [chr16] [step 1.2  ] removed 49.91% of the non-zero entries (2278054/4563983)
2025-01-14 12:49:53.137012 [info     ] [chr16] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:53.160891 [info     ] [chr16] [step 1    ] preprocessing took 126.613ms
2025-01-14 12:49:53.161032 [info     ] [chr16] [step 2    ] topological data analysis
2025-01-14 12:49:53.161091 [info     ] [chr16] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:53.178670 [info     ] [chr16] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:53.178756 [info     ] [chr16] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:53.208640 [info     ] [chr16] [step 2.2.1] lower triangular part
2025-01-14 12:49:53.222317 [info     ] [chr16] [step 2.2.2] upper triangular part
2025-01-14 12:49:53.237804 [info     ] [chr16] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:53.284034 [info     ] [chr16] [step 2.2.3] lower triangular part: number of seed sites reduced from 330 to 299
2025-01-14 12:49:53.284098 [info     ] [chr16] [step 2.2.3] upper triangular part: number of seed sites reduced from 494 to 454
2025-01-14 12:49:53.284148 [info     ] [chr16] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:53.284297 [info     ] [chr16] [step 2.3.1] lower-triangular part: generated 299 candidate stripes
2025-01-14 12:49:53.284355 [info     ] [chr16] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:53.284550 [info     ] [chr16] [step 2.3.2] upper-triangular part: generated 454 candidate stripes
2025-01-14 12:49:53.285103 [info     ] [chr16] [step 2    ] topological data analysis took 124.032ms
2025-01-14 12:49:53.285191 [info     ] [chr16] [step 3    ] shape analysis
2025-01-14 12:49:53.285221 [info     ] [chr16] [step 3.1  ] width estimation
2025-01-14 12:49:53.285243 [info     ] [chr16] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:53.663697 [info     ] [chr16] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:53.663980 [info     ] [chr16] [step 3.1  ] width estimation took 378.752ms
2025-01-14 12:49:53.664030 [info     ] [chr16] [step 3.2  ] height estimation
2025-01-14 12:49:53.664059 [info     ] [chr16] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:54.577776 [info     ] [chr16] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:54.578078 [info     ] [chr16] [step 3.2  ] height estimation took 914.012ms
2025-01-14 12:49:54.578213 [info     ] [chr16] [step 3    ] shape analysis took 1.293s
2025-01-14 12:49:54.578249 [info     ] [chr16] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:54.578280 [info     ] [chr16] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:54.834811 [info     ] [chr16] [step 4    ] statistical analysis and post-processing took 256.514ms
2025-01-14 12:49:54.834933 [info     ] [chr16] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:54.857395 [info     ] [chr16] processing took 2.051s
2025-01-14 12:49:54.857587 [info     ] [chr17] begin processing...
2025-01-14 12:49:55.096834 [info     ] [chr17] [step 1    ] data pre-processing
2025-01-14 12:49:55.096980 [info     ] [chr17] [step 1.1  ] applying log-transformation
2025-01-14 12:49:55.106197 [info     ] [chr17] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:55.193885 [info     ] [chr17] [step 1.2  ] removed 49.92% of the non-zero entries (2369731/4747405)
2025-01-14 12:49:55.194040 [info     ] [chr17] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:55.212893 [info     ] [chr17] [step 1    ] preprocessing took 115.896ms
2025-01-14 12:49:55.213047 [info     ] [chr17] [step 2    ] topological data analysis
2025-01-14 12:49:55.213097 [info     ] [chr17] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:55.230414 [info     ] [chr17] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:55.230514 [info     ] [chr17] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:55.260166 [info     ] [chr17] [step 2.2.1] lower triangular part
2025-01-14 12:49:55.273543 [info     ] [chr17] [step 2.2.2] upper triangular part
2025-01-14 12:49:55.288616 [info     ] [chr17] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:55.330801 [info     ] [chr17] [step 2.2.3] lower triangular part: number of seed sites reduced from 586 to 561
2025-01-14 12:49:55.330861 [info     ] [chr17] [step 2.2.3] upper triangular part: number of seed sites reduced from 548 to 518
2025-01-14 12:49:55.330909 [info     ] [chr17] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:55.331138 [info     ] [chr17] [step 2.3.1] lower-triangular part: generated 561 candidate stripes
2025-01-14 12:49:55.331208 [info     ] [chr17] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:55.331414 [info     ] [chr17] [step 2.3.2] upper-triangular part: generated 518 candidate stripes
2025-01-14 12:49:55.331756 [info     ] [chr17] [step 2    ] topological data analysis took 118.669ms
2025-01-14 12:49:55.331820 [info     ] [chr17] [step 3    ] shape analysis
2025-01-14 12:49:55.331849 [info     ] [chr17] [step 3.1  ] width estimation
2025-01-14 12:49:55.331872 [info     ] [chr17] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:55.821306 [info     ] [chr17] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:55.821537 [info     ] [chr17] [step 3.1  ] width estimation took 489.683ms
2025-01-14 12:49:55.821593 [info     ] [chr17] [step 3.2  ] height estimation
2025-01-14 12:49:55.821633 [info     ] [chr17] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:57.164802 [info     ] [chr17] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:57.165201 [info     ] [chr17] [step 3.2  ] height estimation took 1.344s
2025-01-14 12:49:57.165395 [info     ] [chr17] [step 3    ] shape analysis took 1.834s
2025-01-14 12:49:57.165433 [info     ] [chr17] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:57.165462 [info     ] [chr17] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:49:57.540821 [info     ] [chr17] [step 4    ] statistical analysis and post-processing took 375.346ms
2025-01-14 12:49:57.540946 [info     ] [chr17] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:49:57.569109 [info     ] [chr17] processing took 2.711s
2025-01-14 12:49:57.569311 [info     ] [chr18] begin processing...
2025-01-14 12:49:57.793425 [info     ] [chr18] [step 1    ] data pre-processing
2025-01-14 12:49:57.793567 [info     ] [chr18] [step 1.1  ] applying log-transformation
2025-01-14 12:49:57.802419 [info     ] [chr18] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:49:57.885388 [info     ] [chr18] [step 1.2  ] removed 49.92% of the non-zero entries (2235787/4479156)
2025-01-14 12:49:57.885537 [info     ] [chr18] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:49:57.908233 [info     ] [chr18] [step 1    ] preprocessing took 114.648ms
2025-01-14 12:49:57.908377 [info     ] [chr18] [step 2    ] topological data analysis
2025-01-14 12:49:57.908423 [info     ] [chr18] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:49:57.924653 [info     ] [chr18] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:49:57.924740 [info     ] [chr18] [step 2.2.0] all maxima and their persistence
2025-01-14 12:49:57.953825 [info     ] [chr18] [step 2.2.1] lower triangular part
2025-01-14 12:49:57.966925 [info     ] [chr18] [step 2.2.2] upper triangular part
2025-01-14 12:49:57.982026 [info     ] [chr18] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:49:58.023274 [info     ] [chr18] [step 2.2.3] lower triangular part: number of seed sites reduced from 485 to 480
2025-01-14 12:49:58.023357 [info     ] [chr18] [step 2.2.3] upper triangular part: number of seed sites reduced from 524 to 517
2025-01-14 12:49:58.023409 [info     ] [chr18] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:49:58.023619 [info     ] [chr18] [step 2.3.1] lower-triangular part: generated 480 candidate stripes
2025-01-14 12:49:58.023676 [info     ] [chr18] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:49:58.023873 [info     ] [chr18] [step 2.3.2] upper-triangular part: generated 517 candidate stripes
2025-01-14 12:49:58.024368 [info     ] [chr18] [step 2    ] topological data analysis took 115.956ms
2025-01-14 12:49:58.024450 [info     ] [chr18] [step 3    ] shape analysis
2025-01-14 12:49:58.024480 [info     ] [chr18] [step 3.1  ] width estimation
2025-01-14 12:49:58.024502 [info     ] [chr18] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:49:58.478110 [info     ] [chr18] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:49:58.478395 [info     ] [chr18] [step 3.1  ] width estimation took 453.908ms
2025-01-14 12:49:58.478439 [info     ] [chr18] [step 3.2  ] height estimation
2025-01-14 12:49:58.478469 [info     ] [chr18] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:49:59.702206 [info     ] [chr18] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:49:59.702548 [info     ] [chr18] [step 3.2  ] height estimation took 1.224s
2025-01-14 12:49:59.702693 [info     ] [chr18] [step 3    ] shape analysis took 1.678s
2025-01-14 12:49:59.702729 [info     ] [chr18] [step 4    ] statistical analysis and post-processing
2025-01-14 12:49:59.702761 [info     ] [chr18] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:00.053839 [info     ] [chr18] [step 4    ] statistical analysis and post-processing took 351.065ms
2025-01-14 12:50:00.053960 [info     ] [chr18] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:00.080200 [info     ] [chr18] processing took 2.511s
2025-01-14 12:50:00.080396 [info     ] [chr19] begin processing...
2025-01-14 12:50:00.255736 [info     ] [chr19] [step 1    ] data pre-processing
2025-01-14 12:50:00.255880 [info     ] [chr19] [step 1.1  ] applying log-transformation
2025-01-14 12:50:00.262548 [info     ] [chr19] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:50:00.322916 [info     ] [chr19] [step 1.2  ] removed 49.92% of the non-zero entries (1761044/3527649)
2025-01-14 12:50:00.323059 [info     ] [chr19] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:50:00.336835 [info     ] [chr19] [step 1    ] preprocessing took 80.937ms
2025-01-14 12:50:00.336983 [info     ] [chr19] [step 2    ] topological data analysis
2025-01-14 12:50:00.337029 [info     ] [chr19] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:50:00.349419 [info     ] [chr19] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:50:00.349509 [info     ] [chr19] [step 2.2.0] all maxima and their persistence
2025-01-14 12:50:00.370500 [info     ] [chr19] [step 2.2.1] lower triangular part
2025-01-14 12:50:00.380229 [info     ] [chr19] [step 2.2.2] upper triangular part
2025-01-14 12:50:00.391858 [info     ] [chr19] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:50:00.422550 [info     ] [chr19] [step 2.2.3] lower triangular part: number of seed sites reduced from 547 to 543
2025-01-14 12:50:00.422605 [info     ] [chr19] [step 2.2.3] upper triangular part: number of seed sites reduced from 558 to 555
2025-01-14 12:50:00.422653 [info     ] [chr19] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:50:00.422899 [info     ] [chr19] [step 2.3.1] lower-triangular part: generated 543 candidate stripes
2025-01-14 12:50:00.422961 [info     ] [chr19] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:50:00.423202 [info     ] [chr19] [step 2.3.2] upper-triangular part: generated 555 candidate stripes
2025-01-14 12:50:00.423665 [info     ] [chr19] [step 2    ] topological data analysis took 86.646ms
2025-01-14 12:50:00.423745 [info     ] [chr19] [step 3    ] shape analysis
2025-01-14 12:50:00.423774 [info     ] [chr19] [step 3.1  ] width estimation
2025-01-14 12:50:00.423796 [info     ] [chr19] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:50:00.781360 [info     ] [chr19] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:50:00.781551 [info     ] [chr19] [step 3.1  ] width estimation took 357.773ms
2025-01-14 12:50:00.781586 [info     ] [chr19] [step 3.2  ] height estimation
2025-01-14 12:50:00.781616 [info     ] [chr19] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:50:02.165603 [info     ] [chr19] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:50:02.166001 [info     ] [chr19] [step 3.2  ] height estimation took 1.384s
2025-01-14 12:50:02.166184 [info     ] [chr19] [step 3    ] shape analysis took 1.742s
2025-01-14 12:50:02.166225 [info     ] [chr19] [step 4    ] statistical analysis and post-processing
2025-01-14 12:50:02.166254 [info     ] [chr19] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:02.534826 [info     ] [chr19] [step 4    ] statistical analysis and post-processing took 368.559ms
2025-01-14 12:50:02.534944 [info     ] [chr19] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:02.561652 [info     ] [chr19] processing took 2.481s
2025-01-14 12:50:02.561843 [info     ] [chr20] begin processing...
2025-01-14 12:50:02.759616 [info     ] [chr20] [step 1    ] data pre-processing
2025-01-14 12:50:02.759761 [info     ] [chr20] [step 1.1  ] applying log-transformation
2025-01-14 12:50:02.767328 [info     ] [chr20] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:50:02.834834 [info     ] [chr20] [step 1.2  ] removed 49.92% of the non-zero entries (1943362/3892917)
2025-01-14 12:50:02.834982 [info     ] [chr20] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:50:02.851736 [info     ] [chr20] [step 1    ] preprocessing took 91.957ms
2025-01-14 12:50:02.851877 [info     ] [chr20] [step 2    ] topological data analysis
2025-01-14 12:50:02.851927 [info     ] [chr20] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:50:02.865010 [info     ] [chr20] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:50:02.865103 [info     ] [chr20] [step 2.2.0] all maxima and their persistence
2025-01-14 12:50:02.887962 [info     ] [chr20] [step 2.2.1] lower triangular part
2025-01-14 12:50:02.898370 [info     ] [chr20] [step 2.2.2] upper triangular part
2025-01-14 12:50:02.910582 [info     ] [chr20] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:50:02.943664 [info     ] [chr20] [step 2.2.3] lower triangular part: number of seed sites reduced from 501 to 481
2025-01-14 12:50:02.943719 [info     ] [chr20] [step 2.2.3] upper triangular part: number of seed sites reduced from 411 to 393
2025-01-14 12:50:02.943765 [info     ] [chr20] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:50:02.943972 [info     ] [chr20] [step 2.3.1] lower-triangular part: generated 481 candidate stripes
2025-01-14 12:50:02.944028 [info     ] [chr20] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:50:02.944210 [info     ] [chr20] [step 2.3.2] upper-triangular part: generated 393 candidate stripes
2025-01-14 12:50:02.944622 [info     ] [chr20] [step 2    ] topological data analysis took 92.706ms
2025-01-14 12:50:02.944702 [info     ] [chr20] [step 3    ] shape analysis
2025-01-14 12:50:02.944729 [info     ] [chr20] [step 3.1  ] width estimation
2025-01-14 12:50:02.944751 [info     ] [chr20] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:50:03.264725 [info     ] [chr20] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:50:03.264887 [info     ] [chr20] [step 3.1  ] width estimation took 320.155ms
2025-01-14 12:50:03.264928 [info     ] [chr20] [step 3.2  ] height estimation
2025-01-14 12:50:03.264956 [info     ] [chr20] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:50:04.354917 [info     ] [chr20] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:50:04.355254 [info     ] [chr20] [step 3.2  ] height estimation took 1.090s
2025-01-14 12:50:04.355409 [info     ] [chr20] [step 3    ] shape analysis took 1.411s
2025-01-14 12:50:04.355447 [info     ] [chr20] [step 4    ] statistical analysis and post-processing
2025-01-14 12:50:04.355477 [info     ] [chr20] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:04.660003 [info     ] [chr20] [step 4    ] statistical analysis and post-processing took 304.511ms
2025-01-14 12:50:04.660135 [info     ] [chr20] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:04.684762 [info     ] [chr20] processing took 2.123s
2025-01-14 12:50:04.684961 [info     ] [chr21] begin processing...
2025-01-14 12:50:04.785682 [info     ] [chr21] [step 1    ] data pre-processing
2025-01-14 12:50:04.785829 [info     ] [chr21] [step 1.1  ] applying log-transformation
2025-01-14 12:50:04.789519 [info     ] [chr21] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:50:04.822609 [info     ] [chr21] [step 1.2  ] removed 49.91% of the non-zero entries (975833/1955265)
2025-01-14 12:50:04.822753 [info     ] [chr21] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:50:04.829599 [info     ] [chr21] [step 1    ] preprocessing took 43.755ms
2025-01-14 12:50:04.829740 [info     ] [chr21] [step 2    ] topological data analysis
2025-01-14 12:50:04.829786 [info     ] [chr21] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:50:04.838762 [info     ] [chr21] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:50:04.838853 [info     ] [chr21] [step 2.2.0] all maxima and their persistence
2025-01-14 12:50:04.854426 [info     ] [chr21] [step 2.2.1] lower triangular part
2025-01-14 12:50:04.861623 [info     ] [chr21] [step 2.2.2] upper triangular part
2025-01-14 12:50:04.870422 [info     ] [chr21] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:50:04.894058 [info     ] [chr21] [step 2.2.3] lower triangular part: number of seed sites reduced from 232 to 210
2025-01-14 12:50:04.894123 [info     ] [chr21] [step 2.2.3] upper triangular part: number of seed sites reduced from 220 to 206
2025-01-14 12:50:04.894173 [info     ] [chr21] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:50:04.894287 [info     ] [chr21] [step 2.3.1] lower-triangular part: generated 210 candidate stripes
2025-01-14 12:50:04.894330 [info     ] [chr21] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:50:04.894435 [info     ] [chr21] [step 2.3.2] upper-triangular part: generated 206 candidate stripes
2025-01-14 12:50:04.894828 [info     ] [chr21] [step 2    ] topological data analysis took 65.052ms
2025-01-14 12:50:04.894903 [info     ] [chr21] [step 3    ] shape analysis
2025-01-14 12:50:04.894933 [info     ] [chr21] [step 3.1  ] width estimation
2025-01-14 12:50:04.894956 [info     ] [chr21] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:50:05.008547 [info     ] [chr21] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:50:05.008655 [info     ] [chr21] [step 3.1  ] width estimation took 113.719ms
2025-01-14 12:50:05.008687 [info     ] [chr21] [step 3.2  ] height estimation
2025-01-14 12:50:05.008712 [info     ] [chr21] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:50:05.515499 [info     ] [chr21] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:50:05.515729 [info     ] [chr21] [step 3.2  ] height estimation took 507.012ms
2025-01-14 12:50:05.515817 [info     ] [chr21] [step 3    ] shape analysis took 620.888ms
2025-01-14 12:50:05.515856 [info     ] [chr21] [step 4    ] statistical analysis and post-processing
2025-01-14 12:50:05.515884 [info     ] [chr21] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:05.657974 [info     ] [chr21] [step 4    ] statistical analysis and post-processing took 142.077ms
2025-01-14 12:50:05.658095 [info     ] [chr21] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:05.674466 [info     ] [chr21] processing took 989.456ms
2025-01-14 12:50:05.674658 [info     ] [chr22] begin processing...
2025-01-14 12:50:05.784205 [info     ] [chr22] [step 1    ] data pre-processing
2025-01-14 12:50:05.784349 [info     ] [chr22] [step 1.1  ] applying log-transformation
2025-01-14 12:50:05.788569 [info     ] [chr22] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:50:05.823964 [info     ] [chr22] [step 1.2  ] removed 49.92% of the non-zero entries (1122624/2248894)
2025-01-14 12:50:05.824100 [info     ] [chr22] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:50:05.834043 [info     ] [chr22] [step 1    ] preprocessing took 49.676ms
2025-01-14 12:50:05.834191 [info     ] [chr22] [step 2    ] topological data analysis
2025-01-14 12:50:05.834237 [info     ] [chr22] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:50:05.843481 [info     ] [chr22] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:50:05.843561 [info     ] [chr22] [step 2.2.0] all maxima and their persistence
2025-01-14 12:50:05.858842 [info     ] [chr22] [step 2.2.1] lower triangular part
2025-01-14 12:50:05.865971 [info     ] [chr22] [step 2.2.2] upper triangular part
2025-01-14 12:50:05.874833 [info     ] [chr22] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:50:05.899984 [info     ] [chr22] [step 2.2.3] lower triangular part: number of seed sites reduced from 310 to 285
2025-01-14 12:50:05.900039 [info     ] [chr22] [step 2.2.3] upper triangular part: number of seed sites reduced from 286 to 272
2025-01-14 12:50:05.900091 [info     ] [chr22] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:50:05.900233 [info     ] [chr22] [step 2.3.1] lower-triangular part: generated 285 candidate stripes
2025-01-14 12:50:05.900281 [info     ] [chr22] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:50:05.900406 [info     ] [chr22] [step 2.3.2] upper-triangular part: generated 272 candidate stripes
2025-01-14 12:50:05.900641 [info     ] [chr22] [step 2    ] topological data analysis took 66.417ms
2025-01-14 12:50:05.900689 [info     ] [chr22] [step 3    ] shape analysis
2025-01-14 12:50:05.900724 [info     ] [chr22] [step 3.1  ] width estimation
2025-01-14 12:50:05.900746 [info     ] [chr22] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:50:06.063510 [info     ] [chr22] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:50:06.063631 [info     ] [chr22] [step 3.1  ] width estimation took 162.904ms
2025-01-14 12:50:06.063674 [info     ] [chr22] [step 3.2  ] height estimation
2025-01-14 12:50:06.063704 [info     ] [chr22] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:50:06.779866 [info     ] [chr22] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:50:06.780100 [info     ] [chr22] [step 3.2  ] height estimation took 716.390ms
2025-01-14 12:50:06.780184 [info     ] [chr22] [step 3    ] shape analysis took 879.464ms
2025-01-14 12:50:06.780219 [info     ] [chr22] [step 4    ] statistical analysis and post-processing
2025-01-14 12:50:06.780247 [info     ] [chr22] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:06.980759 [info     ] [chr22] [step 4    ] statistical analysis and post-processing took 200.499ms
2025-01-14 12:50:06.980878 [info     ] [chr22] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:07.000949 [info     ] [chr22] processing took 1.326s
2025-01-14 12:50:07.001145 [info     ] [chrX ] begin processing...
2025-01-14 12:50:07.363495 [info     ] [chrX ] [step 1    ] data pre-processing
2025-01-14 12:50:07.363642 [info     ] [chrX ] [step 1.1  ] applying log-transformation
2025-01-14 12:50:07.378805 [info     ] [chrX ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:50:07.524235 [info     ] [chrX ] [step 1.2  ] removed 49.88% of the non-zero entries (3106705/6228374)
2025-01-14 12:50:07.524381 [info     ] [chrX ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:50:07.557036 [info     ] [chrX ] [step 1    ] preprocessing took 193.376ms
2025-01-14 12:50:07.557198 [info     ] [chrX ] [step 2    ] topological data analysis
2025-01-14 12:50:07.557248 [info     ] [chrX ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:50:07.587442 [info     ] [chrX ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:50:07.587537 [info     ] [chrX ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:50:07.643824 [info     ] [chrX ] [step 2.2.1] lower triangular part
2025-01-14 12:50:07.670405 [info     ] [chrX ] [step 2.2.2] upper triangular part
2025-01-14 12:50:07.700167 [info     ] [chrX ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:50:07.780681 [info     ] [chrX ] [step 2.2.3] lower triangular part: number of seed sites reduced from 1183 to 1097
2025-01-14 12:50:07.780746 [info     ] [chrX ] [step 2.2.3] upper triangular part: number of seed sites reduced from 1142 to 1054
2025-01-14 12:50:07.780797 [info     ] [chrX ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:50:07.781227 [info     ] [chrX ] [step 2.3.1] lower-triangular part: generated 1097 candidate stripes
2025-01-14 12:50:07.781321 [info     ] [chrX ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:50:07.781823 [info     ] [chrX ] [step 2.3.2] upper-triangular part: generated 1054 candidate stripes
2025-01-14 12:50:07.782312 [info     ] [chrX ] [step 2    ] topological data analysis took 225.076ms
2025-01-14 12:50:07.782373 [info     ] [chrX ] [step 3    ] shape analysis
2025-01-14 12:50:07.782404 [info     ] [chrX ] [step 3.1  ] width estimation
2025-01-14 12:50:07.782427 [info     ] [chrX ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:50:09.631726 [info     ] [chrX ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:50:09.632189 [info     ] [chrX ] [step 3.1  ] width estimation took 1.850s
2025-01-14 12:50:09.632247 [info     ] [chrX ] [step 3.2  ] height estimation
2025-01-14 12:50:09.632277 [info     ] [chrX ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:50:12.058483 [info     ] [chrX ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:50:12.059094 [info     ] [chrX ] [step 3.2  ] height estimation took 2.427s
2025-01-14 12:50:12.059399 [info     ] [chrX ] [step 3    ] shape analysis took 4.277s
2025-01-14 12:50:12.059441 [info     ] [chrX ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:50:12.059472 [info     ] [chrX ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:12.671345 [info     ] [chrX ] [step 4    ] statistical analysis and post-processing took 611.860ms
2025-01-14 12:50:12.671465 [info     ] [chrX ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:12.712641 [info     ] [chrX ] processing took 5.711s
2025-01-14 12:50:12.712828 [info     ] [chrY ] begin processing...
2025-01-14 12:50:12.737453 [info     ] [chrY ] [step 1    ] data pre-processing
2025-01-14 12:50:12.737532 [info     ] [chrY ] [step 1.1  ] applying log-transformation
2025-01-14 12:50:12.738391 [info     ] [chrY ] [step 1.2  ] focusing on a neighborhood of the main diagonal
2025-01-14 12:50:12.744015 [info     ] [chrY ] [step 1.2  ] removed 49.81% of the non-zero entries (225595/452955)
2025-01-14 12:50:12.744142 [info     ] [chrY ] [step 1.3  ] projecting interactions onto [1, 0]
2025-01-14 12:50:12.746800 [info     ] [chrY ] [step 1    ] preprocessing took 9.257ms
2025-01-14 12:50:12.746901 [info     ] [chrY ] [step 2    ] topological data analysis
2025-01-14 12:50:12.746948 [info     ] [chrY ] [step 2.1.0] computing global 1D pseudo-distributions...
2025-01-14 12:50:12.754766 [info     ] [chrY ] [step 2.2.0] detection of persistent maxima and corresponding minima for lower- and upper-triangular matrices...
2025-01-14 12:50:12.754818 [info     ] [chrY ] [step 2.2.0] all maxima and their persistence
2025-01-14 12:50:12.769835 [info     ] [chrY ] [step 2.2.1] lower triangular part
2025-01-14 12:50:12.776892 [info     ] [chrY ] [step 2.2.2] upper triangular part
2025-01-14 12:50:12.785390 [info     ] [chrY ] [step 2.2.3] removing seeds overlapping sparse regions
2025-01-14 12:50:12.809839 [info     ] [chrY ] [step 2.2.3] lower triangular part: number of seed sites reduced from 130 to 97
2025-01-14 12:50:12.809891 [info     ] [chrY ] [step 2.2.3] upper triangular part: number of seed sites reduced from 148 to 112
2025-01-14 12:50:12.809936 [info     ] [chrY ] [step 2.3.1] lower-triangular part: generating list of candidate stripes...
2025-01-14 12:50:12.810006 [info     ] [chrY ] [step 2.3.1] lower-triangular part: generated 97 candidate stripes
2025-01-14 12:50:12.810045 [info     ] [chrY ] [step 2.3.2] upper-triangular part: generating list of candidate stripes...
2025-01-14 12:50:12.810121 [info     ] [chrY ] [step 2.3.2] upper-triangular part: generated 112 candidate stripes
2025-01-14 12:50:12.810762 [info     ] [chrY ] [step 2    ] topological data analysis took 63.827ms
2025-01-14 12:50:12.810860 [info     ] [chrY ] [step 3    ] shape analysis
2025-01-14 12:50:12.810889 [info     ] [chrY ] [step 3.1  ] width estimation
2025-01-14 12:50:12.810913 [info     ] [chrY ] [step 3.1.1] estimating candidate stripe widths
2025-01-14 12:50:12.879733 [info     ] [chrY ] [step 3.1.2] updating candidate stripes with width information
2025-01-14 12:50:12.879808 [info     ] [chrY ] [step 3.1  ] width estimation took 68.917ms
2025-01-14 12:50:12.879840 [info     ] [chrY ] [step 3.2  ] height estimation
2025-01-14 12:50:12.879865 [info     ] [chrY ] [step 3.2.1] estimating candidate stripe heights
2025-01-14 12:50:13.084029 [info     ] [chrY ] [step 3.1.2] updating candidate stripes with height information
2025-01-14 12:50:13.084150 [info     ] [chrY ] [step 3.2  ] height estimation took 204.282ms
2025-01-14 12:50:13.084207 [info     ] [chrY ] [step 3    ] shape analysis took 273.320ms
2025-01-14 12:50:13.084239 [info     ] [chrY ] [step 4    ] statistical analysis and post-processing
2025-01-14 12:50:13.084265 [info     ] [chrY ] [step 4.1  ] computing stripe biological descriptors
2025-01-14 12:50:13.141638 [info     ] [chrY ] [step 4    ] statistical analysis and post-processing took 57.369ms
2025-01-14 12:50:13.141699 [info     ] [chrY ] writing results to file "/tmp/4DNFI9GMP2J8.10000.hdf5"
2025-01-14 12:50:13.155257 [info     ] [chrY ] processing took 442.386ms
2025-01-14 12:50:13.155714 [info     ] DONE!
2025-01-14 12:50:13.155781 [info     ] processed 24 chromosomes in 1m:48.153s

Running the above command produces a single output file named 4DNFI9GMP2J8.10000.hdf5.

The path to the output file can be changed by using the --output-file CLI option.

Furthermore, it is possible to save the complete log of a run to a file by specifying the path where to store the log file through the --log-file CLI option.

Finally, stripepy call can generate several diagnostic plots that can be of help to gain more insights into the decisions made by the tool. To generate the diagnostic plots, pass --roi=middle e specify the path to a folder where to store the plots using --plot-dir.

4) Fetch stripes in BEDPE format

The .hdf5 file produced by stripepy call contains various kinds of information, including stripe coordinates, various descriptive statistics, persistence vectors, and more.

While having access to all this information can be useful, usually we are mostly interested in the stripe coordinates, which can be fetched using stripepy view.

# Fetch the first 10 stripes in BEDPE format
user@dev:/tmp$ stripepy view 4DNFI9GMP2J8.10000.hdf5 | head

chr1	910000	960000	chr1	930000	3590000
chr1	1060000	1110000	chr1	1080000	3540000
chr1	1400000	1490000	chr1	1430000	3540000
chr1	1600000	1670000	chr1	880000	1620000
chr1	1670000	1700000	chr1	1680000	2610000
chr1	1730000	1780000	chr1	1750000	2570000
chr1	1890000	1940000	chr1	1920000	3540000
chr1	2020000	2060000	chr1	2020000	3550000
chr1	2070000	2120000	chr1	2090000	3540000
chr1	2170000	2230000	chr1	2190000	3500000

# Redirect stdout to a file
user@dev:/tmp$ stripepy view 4DNFI9GMP2J8.10000.hdf5 > stripes.bedpe

# Compress stripes on the fly before writing to a file
user@dev:/tmp$ stripepy view 4DNFI9GMP2J8.10000.hdf5 | gzip -9 > stripes.bedpe.gz

5) Quickly visualize architectural stripes

It is often a good idea to visually inspect at least some of the stripes to make sure that the used parameters are suitable for the dataset that was given to stripepy call.

We provide a Jupyter notebook (visualize_stripes_with_highlass.ipynb) to facilitate this visual inspection. The notebook expects the input file to be in .mcool format.

If your matrix is in .hic format you can easily convert it to .mcool format using hictk by running hictk convert matrix.hic matrix.mcool. HiGlass cannot visualize single-resolution Cooler files. If you are working with .cool files you can use hictk to generate .mcool files by running hictk zoomify matrix.cool matrix.mcool.

For more details, please refer to hictk's documentation: hictk.readthedocs.io.

We recommend running the notebook using JupyterLab.

Furthermore, the notebook depends on a few Python packages that can be installed with pip. Please make sure that the following packages are installed in a virtual environment that is accessible from Jupyter. Refer to IPython documentation for instructions on how to add a virtual environment to Jupyter.

pip install 'clodius>=0.20,<1' 'hictkpy>=1,<2' 'higlass-python>=1.2,<2'

Next, launch JupyterLab and open notebook visualize_stripes_with_highlass.ipynb.

jupyter lab

Before running the notebook, scroll down to the following cell

mcool = ensure_file_exists("CHANGEME.mcool")
bedpe = ensure_file_exists("CHANGEME.bedpe")

and set the mcool and bedpe variables to the path to the .mcool file used to call stripes and the path to the stripe coordinates extracted with stripepy view, respectively.

mcool = ensure_file_exists("4DNFI9GMP2J8.mcool")
bedpe = ensure_file_exists("stripes.bedpe")

Now you are ready to run all cells.

Running the last cell will display a HiGlass window embedded in the Jupyter notebook (note that the interface may take a while to load).

Generating plots

StripePy comes with a plot subcommand that can be used to generate various kinds of plots.

stripepy plot supports the following subcommands:

• contact-map (cm): plot stripes and other features over the Hi-C matrix
• pseudodistribution (pd): plot the pseudo-distribution over the given region of interest
• stripe-hist (hist): generate and plot the histograms showing the distribution of the stripe heights and widths

stripepy cm takes as input a Hi-C matrix in .cool, .mcool, or .hic format, and optionally the .hdf5 file generated by stripepy call (this parameter is mandatory when highlighting stripes or stripe seeds).

stripepy pd and stripepy hist do not require the Hi-C matrix file, and require the .hdf5 file generated by stripepy call instead.

All three subcommands support specifying a region of interest through the --region option. When the commands are run without specifying the region of interest, stripepy cm and stripepy pd will generate plots for a random 2.5 Mbp region, while stripepy hist will generate histograms using data from the entire genome.

Example usage:

# Plot the pseudo-distribution over a region of interest
stripepy plot pd 4DNFI9GMP2J8.10000.hdf5 /tmp/pseudodistribution.png --region chr2:120100000-122100000

# Plot the histograms using genome-wide data
stripepy plot hist 4DNFI9GMP2J8.10000.hdf5 /tmp/stripe_hist_gw.png

# Plot the Hi-C matrix
stripepy plot cm 4DNFI9GMP2J8.mcool 10000 /tmp/matrix.png

# Plot the Hi-C matrix higlighting the stripe seeds
stripepy plot cm 4DNFI9GMP2J8.mcool 10000 /tmp/matrix_with_seeds.png --stripepy-hdf5 4DNFI9GMP2J8.10000.hdf5 --highlight-seeds

# Plot the Hi-C matrix higlighting the architectural stripes
stripepy plot cm 4DNFI9GMP2J8.mcool 10000 /tmp/matrix_with_stripes.png --stripepy-hdf5 4DNFI9GMP2J8.10000.hdf5 --highlight-stripes

Some example plots generated with stripepy plot can be found in file stripepy-plot-test-images.tar.xz from doi.org/10.5281/zenodo.14283921

Getting help

For any issues regarding StripePy installation, walkthrough, and output interpretation please open a discussion on GitHub.

If you've found a bug or would like to suggest a new feature, please open a new issue instead.

Citing

If you use StripePy in your research, please cite the following publication:

Andrea Raffo, Roberto Rossini, Jonas Paulsen, StripePy: fast and robust characterization of architectural stripes bioRxiv 2024.12.20.629789; doi: https://doi.org/10.1101/2024.12.20.629789

BibTex

@article {stripepy,
  author = {Raffo, Andrea and Rossini, Roberto and Paulsen, Jonas},
  title = {StripePy: fast and robust characterization of architectural stripes},
  elocation-id = {2024.12.20.629789},
  year = {2024},
  doi = {10.1101/2024.12.20.629789},
  publisher = {Cold Spring Harbor Laboratory},
  abstract = {
    Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair.
    Despite their importance, few tools exist for automatic stripe detection.
    We introduce StripePy, which leverages computational geometry methods to identify and analyze architectural stripes in contact maps from Chromosome Conformation Capture experiments like Hi-C and Micro-C.
    StripePy outperforms existing tools, as shown through tests on various datasets and a newly developed simulated benchmark, StripeBench, providing a valuable resource for the community.Competing Interest StatementThe authors have declared no competing interest.@
  },
  URL = {https://www.biorxiv.org/content/early/2024/12/22/2024.12.20.629789},
  eprint = {https://www.biorxiv.org/content/early/2024/12/22/2024.12.20.629789.full.pdf},
  journal = {bioRxiv}
}