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Roberto Rossini edited this page Jul 2, 2023 · 2 revisions

MoDLE can be compiled on most UNIX-like systems, including many Linux distributions and MacOS (10.15+).

Build instructions

Build requirements

Compiling MoDLE requires a compiler toolchain supporting C++17, such as:

  • GCC 8+
  • Clang 8+
  • Apple-Clang 10.0+

Furthermore, the following tools are required:

  • CMake 3.25+
  • Conan 2+
  • git 2.7+
  • make or ninja
  • Python3.6+ (including pip, required to install Conan)

We recommend to install CMake and Conan in a Python virtualenv, but you are of course free to install the build dependencies in any way you want.

python3 -m venv /tmp/venv
/tmp/venv/bin/python3 -m pip install pip setuptools --upgrade
/tmp/venv/bin/python3 -m pip  install 'cmake>=3.20' 'conan>=2' ninja

# NOTE: It's important to activate the venv after installing CMake
. /tmp/venv/bin/activate

whereis cmake  # cmake: /tmp/venv/bin/cmake
whereis conan  # conan: /tmp/venv/bin/conan
whereis ninja  # ninja: /tmp/venv/bin/ninja

cmake --version
conan --version

# Detect compiler toolchain. It is usually a good idea to explicitly set CC and CXX
CC=gcc CXX=g++ conan profile detect --force

Compiling MoDLE on Windows using MSVC is currently not possible. Compiling with MinGW may be possible but has never been tested. If you really want to compile MoDLE on Windows, then you can try to do so using the Windows Subsystem for Linux (WSL).

Getting the source code

Download from the Release page (recommended).

mkdir /tmp/modle
curl -L 'https://github.com/paulsengroup/modle/archive/refs/tags/v1.0.1.tar.gz' | tar --strip-components=1 -C /tmp/modle -xzf -

Using git.

git clone https://github.com/paulsengroup/modle.git /tmp/modle

cd /tmp/modle
git checkout v1.0.1  # Skip this step if you want to build the latest commit from main

Compiling MoDLE

# Activate venv
. /tmp/venv/bin/activate

# Set these variables to the number of CPU cores available on your machine
# You can check this with e.g.
# python -c 'import multiprocessing as mp; print(mp.cpu_count())')
export CONAN_CPU_COUNT=8
export CMAKE_BUILD_PARALLEL_LEVEL=8

# Install/build dependencies with Conan
conan install --build=missing \
              -pr default \
              -s build_type=Release \
              -s compiler.cppstd=17 \
              --output-folder=./build/ \
              .

# This may take a while, as CMake will run Conan to build MoDLE dependencies.
# Do not pass -G Ninja if you want CMake to use make instead of ninja
cmake -DCMAKE_BUILD_TYPE=Release \
      -DCMAKE_PREFIX_PATH="$PWD/build" \
      -DMODLE_ENABLE_TESTING=ON  \
      -G Ninja \
      -S /tmp/modle \
      -B /tmp/modle/build

cmake --build /tmp/modle/build

To override the default compiler used by CMake, pass the following arguments to the first CMake command: -DCMAKE_C_COMPILER=path/to/cc -DCMAKE_CXX_COMPILER=path/to/c++

We highly recommend using the same compiler when running Conan and CMake.

Running automated tests

Steps outlined in this section are optional but highly recommended.

Unit tests

# Activate venv
. /tmp/venv/bin/activate

cd /tmp/modle
ctest --test-dir build/   \
      --schedule-random   \
      --output-on-failure \
      --no-tests=error    \
      --timeout 600       \
      -j8  # Change this to the number of available CPU cores

A successful run of the test suite will produce an output like the following:

user@dev:/tmp/modle$ ctest --test-dir build/ ...
...
125/128 Test #120: ContactMatrix internal: encode/decode roundtrip - LONG ...........................................   Passed   35.05 sec
126/128 Test #117: ContactMatrixSparse serialization - LONG .........................................................   Passed   42.19 sec
127/128 Test #119: ContactMatrixSparse serialization (FP) - LONG ....................................................   Passed   44.71 sec
128/128 Test #118: ContactMatrixSparse serialization (destructive) - LONG ...........................................   Passed   32.53 sec

100% tests passed, 0 tests failed out of 128

Total Test time (real) =  45.83 sec

All tests are expected to pass. Do not ignore test failures!

Troubleshooting test failures If one or more test fail, try the following troubleshooting steps before reaching out for help.
  1. Make sure you are running ctest from the root of the source tree (/tmp/modle if you are following the instructions).
  2. Make sure you are passing the correct build folder to --test-dir. Pass the absolute path if necessary (i.e. --test-dir=/tmp/modle/build/ if you are following the instructions).
  3. Re-run ctest with -j1. This can be necessary on machines with very little memory (e.g. less than 2GB).
  4. Before running ctest, create a temporary folder where your user has read-write permissions and where there are at least 100-200MB of space available. Then set variable TMPDIR to that folder and re-run ctest.
  5. Checksum the test dataset located under test/data/ by running sha256sum -c checksums.sha256. If the checksumming fails or the folder doesn't exist, download and extract the .tar.xz file listed in file cmake/FetchTestDataset.cmake. Make sure you run tar -xf from the root of the repository (/tmp/modle if you are following the instructions).

Example:

# Activate venv
. /tmp/venv/bin/activate

cd /tmp/modle

# Make sure this is the URL listed  in file cmake/FetchTestDataset.cmake
curl -L 'https://zenodo.org/record/7506960/files/modle_test_data.tar.xz?download=1' | tar -xJf -

# This should print "OK" if the check is successful
(cd test/data && sha256sum --quiet -c checksums.sha256 && 2>&1 echo OK)

mkdir ~/modle-test-dir  # Remember to delete this folder

TMPDIR="$HOME/modle-test-dir"      \
ctest --test-dir=/tmp/modle/build/ \
      --schedule-random            \
      --output-on-failure          \
      --no-tests=error             \
      --timeout 600                \
      -j1

# rm -r ~/modle-test-dir

If after trying the above steps the tests are still failing, feel free to start discussion asking for help.

Integration tests

The integration test scripts depend on the following tools:

  • cooler>=0.9
  • pyBigWig
  • xz
  • common UNIX shell commands (namely cmp, diff, grep and mktemp)

cooler can be installed using pip:

/tmp/venv/bin/pip3 install 'cooler>=0.9 pyBigWig'

If not already installed, xz can usually be installed with your system package manager (on some Linux distributions the relevant package is called xz-utils).

# Activate venv
. /tmp/venv/bin/activate

# Test modle
test/scripts/modle_integration_test.sh build/src/modle/modle

# Test modle_tools
test/scripts/modle_tools_transform_integration_test.sh build/src/modle_tools/modle_tools
test/scripts/modle_tools_eval_integration_test.sh build/src/modle_tools/modle_tools
test/scripts/modle_tools_annotate_barriers_integration_test.sh build/src/modle_tools/modle_tools
Sample outputs of successful test runs 
[2023-05-11 11:42:03.315] [info]: running MoDLE v1.0.1
[2023-05-11 11:42:03.315] [info]: complete log will be written to file "/tmp/modle-ci-SpASy09Lp3/out.log"
[2023-05-11 11:42:03.315] [info]: writing simulation parameters to config file "/tmp/modle-ci-SpASy09Lp3/out_config.toml"
[2023-05-11 11:42:03.316] [info]: command: cmake-build-release-llvm-test-release/src/modle/modle sim -c modle/test/data/integration_tests/grch38.chrom.sizes -g modle/test/data/integration_tests/grch38_regions_of_interest.bed -b modle/test/data/integration_tests/grch38_h1_extrusion_barriers.bed.xz -o /tmp/modle-ci-SpASy09Lp3/out -r 20kb --verbose --target-contact-density 20 --ncells 2 --track-1d-lef-position --max-burnin-epochs 5000
[2023-05-11 11:42:03.316] [info]: simulation will use up to 16 out of 16 available CPU cores.
[2023-05-11 11:42:03.316] [info]: using --target-contact-density=20.00 as stopping criterion.
[2023-05-11 11:42:03.316] [info]: contact sampling strategy: tad-plus-loop-with-noise.
[2023-05-11 11:42:03.316] [info]: contact matrix resolution: 20000bp
[2023-05-11 11:42:03.316] [info]: importing chromosomes from "modle/test/data/integration_tests/grch38.chrom.sizes"...
[2023-05-11 11:42:03.317] [info]: imported 24 chromosomes in 697.651us.
[2023-05-11 11:42:03.317] [info]: importing genomic intervals from "modle/test/data/integration_tests/grch38_regions_of_interest.bed"...
[2023-05-11 11:42:03.317] [info]: imported 11 intervals in 319.171us.
[2023-05-11 11:42:03.317] [info]: importing extrusion barriers from "modle/test/data/integration_tests/grch38_h1_extrusion_barriers.bed.xz"...
[2023-05-11 11:42:03.361] [info]: imported 2087 barriers from "modle/test/data/integration_tests/grch38_h1_extrusion_barriers.bed.xz" in 43.849816ms.
[2023-05-11 11:42:03.362] [warning]: simulated size for the following 5 interval(s) is smaller than the simulation diagonal width (3000000 bp). Is this intended?
 - chr17:40200000-42800000: 2600000;
 - chr17:46800000-49300000: 2500000;
 - chr17:60200000-63100000: 2900000;
 - chr17:64600000-66200000: 1600000;
 - chr17:76800000-77200000: 400000;
[2023-05-11 11:42:03.362] [warning]: contact matrix for the following 10 interval(s) appears to be really small (less than 250000 pixels). Is this intended?
 - chr17:3400000-6500000: 23250 pixels
 - chr17:10800000-16100000: 39750 pixels
 - chr17:33500000-39800000: 47250 pixels
 - chr17:40200000-42800000: 19500 pixels
 - chr17:46800000-49300000: 18750 pixels
 - chr17:52100000-59500000: 55500 pixels
 - chr17:60200000-63100000: 21750 pixels
 - chr17:64600000-66200000: 12000 pixels
 - chr17:69100000-72900000: 28500 pixels
 - chr17:76800000-77200000: 3000 pixels
[2023-05-11 11:42:03.362] [info]: spawning IO thread...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W0...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W9...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W2...
[2023-05-11 11:42:03.362] [debug]: [main]: submitting task #0 (chr17:3400000-6500000 cell #0)...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W15...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W4...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W6...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W7...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W8...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W11...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W10...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W13...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W12...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W14...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W1...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W3...
[2023-05-11 11:42:03.362] [debug]: [main]: submitting task #1 (chr17:3400000-6500000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #2 (chr17:10800000-16100000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #3 (chr17:10800000-16100000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #4 (chr17:33500000-39800000 cell #0)...
[2023-05-11 11:42:03.362] [info]: spawning worker thread W5...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #5 (chr17:33500000-39800000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #6 (chr17:40200000-42800000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #7 (chr17:40200000-42800000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #8 (chr17:46800000-49300000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #9 (chr17:46800000-49300000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #10 (chr17:52100000-59500000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #11 (chr17:52100000-59500000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #12 (chr17:60200000-63100000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #13 (chr17:60200000-63100000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #14 (chr17:64600000-66200000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #15 (chr17:64600000-66200000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #16 (chr17:69100000-72900000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #17 (chr17:69100000-72900000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #18 (chr17:76800000-77200000 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #19 (chr17:76800000-77200000 cell #1)...
[2023-05-11 11:42:03.363] [debug]: [W7]: begin processing task 11 (chr17:52100000-59500000 cell #1, 0x7dba39cdd272b1bf83640f92d867800050ed7654ab1cd71def39ddaa685862a4)...
[2023-05-11 11:42:03.363] [debug]: [W0]: begin processing task 1 (chr17:3400000-6500000 cell #1, 0xf989845f1d5e7366868d488424e5721f7a8c93f84c9e969febf7e8207c97060c)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:33500000-39800000: simulating ~11667 epochs across 2 cells using 126 LEFs and 137 barriers (~5833 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W12]: begin processing task 4 (chr17:33500000-39800000 cell #0, 0xacf52581c195c57e39e98ddbe38add37f6549f1ee8b840846975a121751c865b)...
[2023-05-11 11:42:03.363] [debug]: [W14]: begin processing task 3 (chr17:10800000-16100000 cell #1, 0x75fe0e29cac63fafb2f7295e5d2ada8143d515f87bdc6b45a329fcc1de2bad76)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:52100000-59500000: simulating ~11684 epochs across 2 cells using 148 LEFs and 106 barriers (~5842 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W2]: begin processing task 10 (chr17:52100000-59500000 cell #0, 0xc8352a6614980a95ad7d7142970c9e77216ea23c47e035be5eb926e3f770e34b)...
[2023-05-11 11:42:03.363] [debug]: [W10]: begin processing task 7 (chr17:40200000-42800000 cell #1, 0x77c8bde3ddf1faeeb8f5c4b09ed93c30392bfffe57974f1528f9d51d3eb7ad4d)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:10800000-16100000: simulating ~11691 epochs across 2 cells using 106 LEFs and 67 barriers (~5845 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W9]: begin processing task 2 (chr17:10800000-16100000 cell #0, 0x855f4ecc138b144575074359f6ee20516a35db461ce6a6986508bbafe169de0d)...
[2023-05-11 11:42:03.363] [debug]: [W1]: begin processing task 9 (chr17:46800000-49300000 cell #1, 0x35f79d9403df23f29508e06f1e7c8576d67f1e279c958778bf4da4a3b577f069)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:3400000-6500000: simulating ~11625 epochs across 2 cells using 62 LEFs and 80 barriers (~5812 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W3]: begin processing task 13 (chr17:60200000-63100000 cell #1, 0xa1f8b81598ef32e1bb5f939da04508662e1824121ae114051199c032087a6627)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:60200000-63100000: simulating ~11757 epochs across 2 cells using 58 LEFs and 35 barriers (~5878 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W6]: begin processing task 5 (chr17:33500000-39800000 cell #1, 0x635ba9dffc765bb40bf4cebcb302a6b3436beaf044a7fc9200f03ee5f9c538f0)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:64600000-66200000: simulating ~12000 epochs across 2 cells using 32 LEFs and 24 barriers (~6000 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W5]: begin processing task 15 (chr17:64600000-66200000 cell #1, 0x37aa169907199d414d7b15425a3a5cc6d5f7a22caebf44178323862575834445)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:40200000-42800000: simulating ~11818 epochs across 2 cells using 52 LEFs and 77 barriers (~5909 epochs per cell)...
[2023-05-11 11:42:03.363] [info]: begin processing chr17:46800000-49300000: simulating ~11719 epochs across 2 cells using 50 LEFs and 65 barriers (~5859 epochs per cell)...
[2023-05-11 11:42:03.363] [debug]: [W11]: begin processing task 8 (chr17:46800000-49300000 cell #0, 0xf9f36a5d81f9efbe2e7e9007e7e62b88d2483867a3636e959d992113c304e749)...
[2023-05-11 11:42:03.364] [debug]: allocating a 150x80 contact matrix...
[2023-05-11 11:42:03.363] [debug]: [main]: submitting task #20 (chr19:0-58617616 cell #0)...
[2023-05-11 11:42:03.363] [debug]: [W13]: begin processing task 12 (chr17:60200000-63100000 cell #0, 0x553b7b0c46f1c8bb42f6a71bffabe0bb71fc30ace94b900f4db4285c550f184d)...
[2023-05-11 11:42:03.364] [debug]: allocating a vector of size 80...
[2023-05-11 11:42:03.365] [debug]: allocating a 150x130 contact matrix...
[2023-05-11 11:42:03.365] [debug]: allocating a vector of size 130...
[2023-05-11 11:42:03.365] [debug]: allocating a 150x265 contact matrix...
[2023-05-11 11:42:03.363] [debug]: [W8]: begin processing task 14 (chr17:64600000-66200000 cell #0, 0x2c0d706739eb7bf9687d641e3c1716c96368835d83688ca6e31758f0fa227b26)...
[2023-05-11 11:42:03.365] [debug]: [main]: submitting task #21 (chr19:0-58617616 cell #1)...
[2023-05-11 11:42:03.365] [debug]: waiting for worker threads to return...
[2023-05-11 11:42:03.364] [debug]: [W4]: begin processing task 6 (chr17:40200000-42800000 cell #0, 0x6c4136a584f59c48aca20dcabbe48501963aad40b7fef2445473d046bb24f948)...
[2023-05-11 11:42:03.366] [debug]: allocating a vector of size 265...
[2023-05-11 11:42:03.366] [debug]: allocating a 150x145 contact matrix...
[2023-05-11 11:42:03.366] [debug]: allocating a vector of size 145...
[2023-05-11 11:42:03.367] [debug]: allocating a 150x155 contact matrix...
[2023-05-11 11:42:03.367] [debug]: allocating a vector of size 155...
[2023-05-11 11:42:03.368] [debug]: allocating a 150x125 contact matrix...
[2023-05-11 11:42:03.368] [debug]: allocating a vector of size 125...
[2023-05-11 11:42:03.368] [debug]: allocating a 150x315 contact matrix...
[2023-05-11 11:42:03.369] [debug]: allocating a vector of size 315...
[2023-05-11 11:42:03.373] [debug]: allocating a 150x370 contact matrix...
[2023-05-11 11:42:03.363] [debug]: [W15]: begin processing task 0 (chr17:3400000-6500000 cell #0, 0x6e705dd633f92ffa562fa5b8ad800ff4b323454db6b95b1434b52875d2961d9e)...
[2023-05-11 11:42:03.380] [debug]: allocating a vector of size 370...
[2023-05-11 11:42:03.468] [debug]: [W5]: finished processing task 15 (chr17:64600000-66200000 cell #1, 0x37aa169907199d414d7b15425a3a5cc6d5f7a22caebf44178323862575834445): collected 120000 interactions throughout 6851 epochs (148 burnin epochs)
[2023-05-11 11:42:03.468] [info]: begin processing chr17:69100000-72900000: simulating ~11633 epochs across 2 cells using 76 LEFs and 43 barriers (~5816 epochs per cell)...
[2023-05-11 11:42:03.468] [debug]: [W5]: begin processing task 16 (chr17:69100000-72900000 cell #0, 0xc35a95ef10d1fcb0bb6c84546f3b5c771ef2d412b3e39efe52a284b74dc37fbc)...
[2023-05-11 11:42:03.472] [debug]: [W8]: finished processing task 14 (chr17:64600000-66200000 cell #0, 0x2c0d706739eb7bf9687d641e3c1716c96368835d83688ca6e31758f0fa227b26): collected 120000 interactions throughout 7044 epochs (351 burnin epochs)
[2023-05-11 11:42:03.473] [debug]: [W8]: begin processing task 17 (chr17:69100000-72900000 cell #1, 0x3cfd0646005565a3616be293793ae8b47a183af2bd26de648e58238985c59fdd)...
[2023-05-11 11:42:03.477] [debug]: allocating a 150x190 contact matrix...
[2023-05-11 11:42:03.477] [debug]: allocating a vector of size 190...
[2023-05-11 11:42:03.524] [debug]: [W1]: finished processing task 9 (chr17:46800000-49300000 cell #1, 0x35f79d9403df23f29508e06f1e7c8576d67f1e279c958778bf4da4a3b577f069): collected 187500 interactions throughout 6531 epochs (359 burnin epochs)
[2023-05-11 11:42:03.524] [info]: begin processing chr17:76800000-77200000: simulating ~12000 epochs across 2 cells using 8 LEFs and 12 barriers (~6000 epochs per cell)...
[2023-05-11 11:42:03.524] [debug]: [W1]: begin processing task 18 (chr17:76800000-77200000 cell #0, 0x01bc4ddbec98829a30ac06832dd289e4378615b4cc7e1f7d4a52a8360d484329)...
[2023-05-11 11:42:03.525] [debug]: allocating a 150x20 contact matrix...
[2023-05-11 11:42:03.525] [debug]: allocating a vector of size 20...
[2023-05-11 11:42:03.529] [debug]: [W11]: finished processing task 8 (chr17:46800000-49300000 cell #0, 0xf9f36a5d81f9efbe2e7e9007e7e62b88d2483867a3636e959d992113c304e749): collected 187500 interactions throughout 6582 epochs (416 burnin epochs)
[2023-05-11 11:42:03.530] [debug]: [W11]: begin processing task 19 (chr17:76800000-77200000 cell #1, 0x90d2ff862cd23ec1073aee34c927b088d68a33877b76c3baca2d97868c1fc137)...
[2023-05-11 11:42:03.541] [debug]: [W13]: finished processing task 12 (chr17:60200000-63100000 cell #0, 0x553b7b0c46f1c8bb42f6a71bffabe0bb71fc30ace94b900f4db4285c550f184d): collected 217500 interactions throughout 6514 epochs (187 burnin epochs)
[2023-05-11 11:42:03.541] [info]: begin processing chr19:0-58617616: simulating ~11724 epochs across 2 cells using 1172 LEFs and 1441 barriers (~5862 epochs per cell)...
[2023-05-11 11:42:03.541] [debug]: [W13]: begin processing task 20 (chr19:0-58617616 cell #0, 0x9b93afbc98c209686dc41783d8e0039a0d048f6edd9719becab4bed89163951a)...
[2023-05-11 11:42:03.543] [debug]: [W3]: finished processing task 13 (chr17:60200000-63100000 cell #1, 0xa1f8b81598ef32e1bb5f939da04508662e1824121ae114051199c032087a6627): collected 217500 interactions throughout 6755 epochs (419 burnin epochs)
[2023-05-11 11:42:03.543] [debug]: [W3]: begin processing task 21 (chr19:0-58617616 cell #1, 0xbf6bff8c51e1ce920d4da20970373f04dc2177a111e26e0be5454e2985187a6f)...
[2023-05-11 11:42:03.550] [debug]: [W4]: finished processing task 6 (chr17:40200000-42800000 cell #0, 0x6c4136a584f59c48aca20dcabbe48501963aad40b7fef2445473d046bb24f948): collected 195000 interactions throughout 6510 epochs (230 burnin epochs)
[2023-05-11 11:42:03.552] [debug]: [W10]: finished processing task 7 (chr17:40200000-42800000 cell #1, 0x77c8bde3ddf1faeeb8f5c4b09ed93c30392bfffe57974f1528f9d51d3eb7ad4d): collected 195000 interactions throughout 6435 epochs (165 burnin epochs)
[2023-05-11 11:42:03.561] [debug]: [W1]: finished processing task 18 (chr17:76800000-77200000 cell #0, 0x01bc4ddbec98829a30ac06832dd289e4378615b4cc7e1f7d4a52a8360d484329): collected 30000 interactions throughout 9285 epochs (226 burnin epochs)
[2023-05-11 11:42:03.569] [debug]: [W11]: finished processing task 19 (chr17:76800000-77200000 cell #1, 0x90d2ff862cd23ec1073aee34c927b088d68a33877b76c3baca2d97868c1fc137): collected 30000 interactions throughout 9395 epochs (370 burnin epochs)
[2023-05-11 11:42:03.574] [debug]: [W0]: finished processing task 1 (chr17:3400000-6500000 cell #1, 0xf989845f1d5e7366868d488424e5721f7a8c93f84c9e969febf7e8207c97060c): collected 232500 interactions throughout 6361 epochs (263 burnin epochs)
[2023-05-11 11:42:03.581] [debug]: allocating a 150x2931 contact matrix...
[2023-05-11 11:42:03.583] [debug]: allocating a vector of size 2931...
[2023-05-11 11:42:03.607] [debug]: [W15]: finished processing task 0 (chr17:3400000-6500000 cell #0, 0x6e705dd633f92ffa562fa5b8ad800ff4b323454db6b95b1434b52875d2961d9e): collected 232500 interactions throughout 6429 epochs (334 burnin epochs)
[2023-05-11 11:42:03.608] [info]: [io] writing contacts for chr17:3400000-6500000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.630] [info]: [io]: written 465000 contacts for chr17:3400000-6500000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 22.840537ms (0.00M nnz out of 0.02M pixels).
[2023-05-11 11:42:03.630] [info]: [io]: writing 1D LEF occupancy profile for chr17:3400000-6500000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.630] [info]: [io]: writing 1D LEF occupancy profile for chr17:3400000-6500000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 29.038us
[2023-05-11 11:42:03.630] [debug]: deallocating a 150x155 contact matrix...
[2023-05-11 11:42:03.630] [debug]: deallocating a vector of size 155...
[2023-05-11 11:42:03.651] [debug]: [W4]: all tasks have been processed: returning!
[2023-05-11 11:42:03.654] [debug]: [W10]: all tasks have been processed: returning!
[2023-05-11 11:42:03.661] [debug]: [W1]: all tasks have been processed: returning!
[2023-05-11 11:42:03.669] [debug]: [W11]: all tasks have been processed: returning!
[2023-05-11 11:42:03.674] [debug]: [W0]: all tasks have been processed: returning!
[2023-05-11 11:42:03.683] [debug]: [W14]: finished processing task 3 (chr17:10800000-16100000 cell #1, 0x75fe0e29cac63fafb2f7295e5d2ada8143d515f87bdc6b45a329fcc1de2bad76): collected 397500 interactions throughout 6194 epochs (154 burnin epochs)
[2023-05-11 11:42:03.708] [debug]: [W15]: all tasks have been processed: returning!
[2023-05-11 11:42:03.717] [debug]: [W8]: finished processing task 17 (chr17:69100000-72900000 cell #1, 0x3cfd0646005565a3616be293793ae8b47a183af2bd26de648e58238985c59fdd): collected 285000 interactions throughout 6380 epochs (240 burnin epochs)
[2023-05-11 11:42:03.732] [debug]: [W5]: finished processing task 16 (chr17:69100000-72900000 cell #0, 0xc35a95ef10d1fcb0bb6c84546f3b5c771ef2d412b3e39efe52a284b74dc37fbc): collected 285000 interactions throughout 6679 epochs (529 burnin epochs)
[2023-05-11 11:42:03.732] [debug]: [W9]: finished processing task 2 (chr17:10800000-16100000 cell #0, 0x855f4ecc138b144575074359f6ee20516a35db461ce6a6986508bbafe169de0d): collected 397500 interactions throughout 6430 epochs (399 burnin epochs)
[2023-05-11 11:42:03.732] [info]: [io] writing contacts for chr17:10800000-16100000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.733] [debug]: [W12]: finished processing task 4 (chr17:33500000-39800000 cell #0, 0xacf52581c195c57e39e98ddbe38add37f6549f1ee8b840846975a121751c865b): collected 472500 interactions throughout 6337 epochs (399 burnin epochs)
[2023-05-11 11:42:03.744] [info]: [io]: written 795000 contacts for chr17:10800000-16100000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 11.809805ms (0.01M nnz out of 0.04M pixels).
[2023-05-11 11:42:03.744] [info]: [io]: writing 1D LEF occupancy profile for chr17:10800000-16100000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.744] [info]: [io]: writing 1D LEF occupancy profile for chr17:10800000-16100000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 203.41us
[2023-05-11 11:42:03.744] [debug]: deallocating a 150x265 contact matrix...
[2023-05-11 11:42:03.744] [debug]: deallocating a vector of size 265...
[2023-05-11 11:42:03.756] [debug]: [W6]: finished processing task 5 (chr17:33500000-39800000 cell #1, 0x635ba9dffc765bb40bf4cebcb302a6b3436beaf044a7fc9200f03ee5f9c538f0): collected 472500 interactions throughout 6145 epochs (205 burnin epochs)
[2023-05-11 11:42:03.756] [info]: [io] writing contacts for chr17:33500000-39800000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.757] [debug]: [W2]: finished processing task 10 (chr17:52100000-59500000 cell #0, 0xc8352a6614980a95ad7d7142970c9e77216ea23c47e035be5eb926e3f770e34b): collected 555000 interactions throughout 6320 epochs (353 burnin epochs)
[2023-05-11 11:42:03.768] [info]: [io]: written 945000 contacts for chr17:33500000-39800000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 11.162817ms (0.01M nnz out of 0.05M pixels).
[2023-05-11 11:42:03.768] [info]: [io]: writing 1D LEF occupancy profile for chr17:33500000-39800000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.768] [info]: [io]: writing 1D LEF occupancy profile for chr17:33500000-39800000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 160.875us
[2023-05-11 11:42:03.768] [debug]: deallocating a 150x315 contact matrix...
[2023-05-11 11:42:03.768] [debug]: deallocating a vector of size 315...
[2023-05-11 11:42:03.768] [info]: [io] writing contacts for chr17:40200000-42800000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.777] [info]: [io]: written 390000 contacts for chr17:40200000-42800000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 8.85221ms (0.00M nnz out of 0.02M pixels).
[2023-05-11 11:42:03.777] [info]: [io]: writing 1D LEF occupancy profile for chr17:40200000-42800000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.777] [info]: [io]: writing 1D LEF occupancy profile for chr17:40200000-42800000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 172.761us
[2023-05-11 11:42:03.777] [debug]: deallocating a 150x130 contact matrix...
[2023-05-11 11:42:03.777] [debug]: deallocating a vector of size 130...
[2023-05-11 11:42:03.777] [info]: [io] writing contacts for chr17:46800000-49300000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.783] [debug]: [W14]: all tasks have been processed: returning!
[2023-05-11 11:42:03.786] [info]: [io]: written 375000 contacts for chr17:46800000-49300000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 9.009251ms (0.00M nnz out of 0.02M pixels).
[2023-05-11 11:42:03.786] [info]: [io]: writing 1D LEF occupancy profile for chr17:46800000-49300000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.786] [info]: [io]: writing 1D LEF occupancy profile for chr17:46800000-49300000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 81.686us
[2023-05-11 11:42:03.786] [debug]: deallocating a 150x125 contact matrix...
[2023-05-11 11:42:03.786] [debug]: deallocating a vector of size 125...
[2023-05-11 11:42:03.797] [debug]: [W7]: finished processing task 11 (chr17:52100000-59500000 cell #1, 0x7dba39cdd272b1bf83640f92d867800050ed7654ab1cd71def39ddaa685862a4): collected 555000 interactions throughout 6293 epochs (323 burnin epochs)
[2023-05-11 11:42:03.797] [info]: [io] writing contacts for chr17:52100000-59500000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.809] [info]: [io]: written 1110000 contacts for chr17:52100000-59500000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 12.295641ms (0.01M nnz out of 0.06M pixels).
[2023-05-11 11:42:03.809] [info]: [io]: writing 1D LEF occupancy profile for chr17:52100000-59500000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.810] [info]: [io]: writing 1D LEF occupancy profile for chr17:52100000-59500000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 111.221us
[2023-05-11 11:42:03.810] [debug]: deallocating a 150x370 contact matrix...
[2023-05-11 11:42:03.810] [debug]: deallocating a vector of size 370...
[2023-05-11 11:42:03.810] [info]: [io] writing contacts for chr17:60200000-63100000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.817] [debug]: [W8]: all tasks have been processed: returning!
[2023-05-11 11:42:03.819] [info]: [io]: written 435000 contacts for chr17:60200000-63100000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 9.643798ms (0.01M nnz out of 0.02M pixels).
[2023-05-11 11:42:03.819] [info]: [io]: writing 1D LEF occupancy profile for chr17:60200000-63100000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.819] [info]: [io]: writing 1D LEF occupancy profile for chr17:60200000-63100000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 133.274us
[2023-05-11 11:42:03.819] [debug]: deallocating a 150x145 contact matrix...
[2023-05-11 11:42:03.819] [debug]: deallocating a vector of size 145...
[2023-05-11 11:42:03.819] [info]: [io] writing contacts for chr17:64600000-66200000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.827] [info]: [io]: written 240000 contacts for chr17:64600000-66200000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 7.99357ms (0.00M nnz out of 0.01M pixels).
[2023-05-11 11:42:03.827] [info]: [io]: writing 1D LEF occupancy profile for chr17:64600000-66200000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.828] [info]: [io]: writing 1D LEF occupancy profile for chr17:64600000-66200000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 82.026us
[2023-05-11 11:42:03.828] [debug]: deallocating a 150x80 contact matrix...
[2023-05-11 11:42:03.828] [debug]: deallocating a vector of size 80...
[2023-05-11 11:42:03.828] [info]: [io] writing contacts for chr17:69100000-72900000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.832] [debug]: [W5]: all tasks have been processed: returning!
[2023-05-11 11:42:03.832] [debug]: [W9]: all tasks have been processed: returning!
[2023-05-11 11:42:03.833] [debug]: [W12]: all tasks have been processed: returning!
[2023-05-11 11:42:03.838] [info]: [io]: written 570000 contacts for chr17:69100000-72900000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 10.105671ms (0.01M nnz out of 0.03M pixels).
[2023-05-11 11:42:03.838] [info]: [io]: writing 1D LEF occupancy profile for chr17:69100000-72900000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.838] [info]: [io]: writing 1D LEF occupancy profile for chr17:69100000-72900000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 67.837us
[2023-05-11 11:42:03.838] [debug]: deallocating a 150x190 contact matrix...
[2023-05-11 11:42:03.838] [debug]: deallocating a vector of size 190...
[2023-05-11 11:42:03.838] [info]: [io] writing contacts for chr17:76800000-77200000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:03.846] [info]: [io]: written 60000 contacts for chr17:76800000-77200000 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 7.887678ms (0.00M nnz out of 0.00M pixels).
[2023-05-11 11:42:03.846] [info]: [io]: writing 1D LEF occupancy profile for chr17:76800000-77200000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:03.846] [info]: [io]: writing 1D LEF occupancy profile for chr17:76800000-77200000 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 98.888us
[2023-05-11 11:42:03.846] [debug]: deallocating a 150x20 contact matrix...
[2023-05-11 11:42:03.846] [debug]: deallocating a vector of size 20...
[2023-05-11 11:42:03.857] [debug]: [W6]: all tasks have been processed: returning!
[2023-05-11 11:42:03.857] [debug]: [W2]: all tasks have been processed: returning!
[2023-05-11 11:42:03.897] [debug]: [W7]: all tasks have been processed: returning!
[2023-05-11 11:42:06.020] [debug]: [W3]: finished processing task 21 (chr19:0-58617616 cell #1, 0xbf6bff8c51e1ce920d4da20970373f04dc2177a111e26e0be5454e2985187a6f): collected 4396500 interactions throughout 6033 epochs (154 burnin epochs)
[2023-05-11 11:42:06.033] [debug]: [W13]: finished processing task 20 (chr19:0-58617616 cell #0, 0x9b93afbc98c209686dc41783d8e0039a0d048f6edd9719becab4bed89163951a): collected 4396500 interactions throughout 6153 epochs (274 burnin epochs)
[2023-05-11 11:42:06.033] [info]: [io] writing contacts for chr19:0-58617616 to file "/tmp/modle-ci-SpASy09Lp3/out.cool"...
[2023-05-11 11:42:06.066] [info]: [io]: written 8793000 contacts for chr19:0-58617616 to file "/tmp/modle-ci-SpASy09Lp3/out.cool" in 33.047737ms (0.10M nnz out of 0.44M pixels).
[2023-05-11 11:42:06.066] [info]: [io]: writing 1D LEF occupancy profile for chr19:0-58617616 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw"...
[2023-05-11 11:42:06.066] [info]: [io]: writing 1D LEF occupancy profile for chr19:0-58617616 to file "/tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw" took 126.597us
[2023-05-11 11:42:06.066] [debug]: deallocating a 150x2931 contact matrix...
[2023-05-11 11:42:06.066] [debug]: deallocating a vector of size 2931...
[2023-05-11 11:42:06.121] [debug]: [W3]: all tasks have been processed: returning!
[2023-05-11 11:42:06.133] [debug]: [W13]: all tasks have been processed: returning!
[2023-05-11 11:42:06.133] [debug]: waiting for io threads to return...
[2023-05-11 11:42:06.133] [debug]: all background threads returned! Checking if any exception have been raised...
[2023-05-11 11:42:06.133] [debug]: context manager shutdown was successful.
[2023-05-11 11:42:06.133] [info]: simulation terminated without errors in 2.817521006s!

Bye.
Comparing /tmp/modle-ci-SpASy09Lp3/out.cool with modle/test/data/integration_tests/modle_sim_reference_001.cool...
Files are identical
Comparing modle/test/data/integration_tests/modle_sim_reference_001.bw with /tmp/modle-ci-SpASy09Lp3/out_lef_1d_occupancy.bw...
Files are identical

### PASS ###


[2023-05-11 11:44:11.676] [info]: Computing metric(s) for the following 24 intervals:
 - chr1:0-248956422
 - chr2:0-242193529
 - chr3:0-198295559
 - chr4:0-190214555
 - chr5:0-181538259
 - chr6:0-170805979
 - chr7:0-159345973
 - chr8:0-145138636
 - chr9:0-138394717
 - chr10:0-133797422
 - chr11:0-135086622
 - chr12:0-133275309
 - chr13:0-114364328
 - chr14:0-107043718
 - chr15:0-101991189
 - chr16:0-90338345
 - chr17:0-83257441
 - chr18:0-80373285
 - chr19:0-58617616
 - chr20:0-64444167
 - chr21:0-46709983
 - chr22:0-50818468
 - chrX:0-156040895
 - chrY:0-57227415
[2023-05-11 11:44:11.683] [warning]: Read 0 contacts for chr1:248956422. SKIPPING!
[2023-05-11 11:44:11.685] [warning]: Read 0 contacts for chr2:242193529. SKIPPING!
[2023-05-11 11:44:11.687] [warning]: Read 0 contacts for chr3:198295559. SKIPPING!
[2023-05-11 11:44:11.688] [warning]: Read 0 contacts for chr4:190214555. SKIPPING!
[2023-05-11 11:44:11.690] [warning]: Read 0 contacts for chr5:181538259. SKIPPING!
[2023-05-11 11:44:11.691] [warning]: Read 0 contacts for chr6:170805979. SKIPPING!
[2023-05-11 11:44:11.693] [warning]: Read 0 contacts for chr7:159345973. SKIPPING!
[2023-05-11 11:44:11.694] [warning]: Read 0 contacts for chr8:145138636. SKIPPING!
[2023-05-11 11:44:11.696] [warning]: Read 0 contacts for chr9:138394717. SKIPPING!
[2023-05-11 11:44:11.697] [warning]: Read 0 contacts for chr10:133797422. SKIPPING!
[2023-05-11 11:44:11.699] [warning]: Read 0 contacts for chr11:135086622. SKIPPING!
[2023-05-11 11:44:11.701] [warning]: Read 0 contacts for chr12:133275309. SKIPPING!
[2023-05-11 11:44:11.702] [warning]: Read 0 contacts for chr13:114364328. SKIPPING!
[2023-05-11 11:44:11.704] [warning]: Read 0 contacts for chr14:107043718. SKIPPING!
[2023-05-11 11:44:11.705] [warning]: Read 0 contacts for chr15:101991189. SKIPPING!
[2023-05-11 11:44:11.707] [warning]: Read 0 contacts for chr16:90338345. SKIPPING!
[2023-05-11 11:44:11.708] [warning]: Read 0 contacts for chr17:83257441. SKIPPING!
[2023-05-11 11:44:11.710] [warning]: Read 0 contacts for chr18:80373285. SKIPPING!
[2023-05-11 11:44:11.711] [warning]: Read 0 contacts for chr19:58617616. SKIPPING!
[2023-05-11 11:44:11.711] [info]: Reading contacts for chr20:64444167...
[2023-05-11 11:44:11.721] [info]: Read 56772 contacts for chr20:64444167 in 9.592302ms
[2023-05-11 11:44:11.722] [info]: Custom metric for vertical stripes from interval chr20:0-64444167 computed in 614.392us.
[2023-05-11 11:44:11.723] [info]: Custom metric for horizontal stripes from interval chr20:0-64444167 computed in 1.970983ms.
[2023-05-11 11:44:11.738] [info]: 2578 values have been written to files "out_custom_score_custom_metric_vertical.{tsv.gz,bw}" in 16.538823ms.
[2023-05-11 11:44:11.740] [info]: 2578 values have been written to files "out_custom_score_custom_metric_horizontal.{tsv.gz,bw}" in 17.294496ms.
[2023-05-11 11:44:11.741] [warning]: Read 0 contacts for chr21:46709983. SKIPPING!
[2023-05-11 11:44:11.741] [warning]: Read 0 contacts for chr22:50818468. SKIPPING!
[2023-05-11 11:44:11.741] [warning]: Read 0 contacts for chrX:156040895. SKIPPING!
[2023-05-11 11:44:11.741] [warning]: Read 0 contacts for chrY:57227415. SKIPPING!
[2023-05-11 11:44:11.741] [info]: DONE in 101.752652ms!
Comparing modle/test/data/integration_tests/4DNFI9GMP2J8_vs_4DNFIFJH2524_mt_eval_custom_score_custom_metric_horizontal.bw with /tmp/modle-tools-E2x3Ia8BMm/out_custom_score_custom_metric_horizontal.bw...
Files are identical
Comparing modle/test/data/integration_tests/4DNFI9GMP2J8_vs_4DNFIFJH2524_mt_eval_custom_score_custom_metric_vertical.bw with /tmp/modle-tools-E2x3Ia8BMm/out_custom_score_custom_metric_vertical.bw...
Files are identical
Comparing modle/test/data/integration_tests/4DNFI9GMP2J8_vs_4DNFIFJH2524_mt_eval_custom_score_custom_metric_horizontal.tsv.gz with /tmp/modle-tools-E2x3Ia8BMm/out_custom_score_custom_metric_horizontal.tsv.gz...
Files are identical
Comparing modle/test/data/integration_tests/4DNFI9GMP2J8_vs_4DNFIFJH2524_mt_eval_custom_score_custom_metric_vertical.tsv.gz with /tmp/modle-tools-E2x3Ia8BMm/out_custom_score_custom_metric_vertical.tsv.gz...
Files are identical

### PASS ###


[2023-05-11 11:44:34.756] [info]: transforming contacts from Cooler at URI "modle/test/data/integration_tests/4DNFI9GMP2J8_chr20_25kbp.cool"...
[2023-05-11 11:44:34.763] [warning]: read 0 contacts for chr1. SKIPPING!
[2023-05-11 11:44:34.765] [warning]: read 0 contacts for chr2. SKIPPING!
[2023-05-11 11:44:34.766] [warning]: read 0 contacts for chr3. SKIPPING!
[2023-05-11 11:44:34.768] [warning]: read 0 contacts for chr4. SKIPPING!
[2023-05-11 11:44:34.769] [warning]: read 0 contacts for chr5. SKIPPING!
[2023-05-11 11:44:34.771] [warning]: read 0 contacts for chr6. SKIPPING!
[2023-05-11 11:44:34.772] [warning]: read 0 contacts for chr7. SKIPPING!
[2023-05-11 11:44:34.774] [warning]: read 0 contacts for chr8. SKIPPING!
[2023-05-11 11:44:34.775] [warning]: read 0 contacts for chr9. SKIPPING!
[2023-05-11 11:44:34.777] [warning]: read 0 contacts for chr10. SKIPPING!
[2023-05-11 11:44:34.778] [warning]: read 0 contacts for chr11. SKIPPING!
[2023-05-11 11:44:34.780] [warning]: read 0 contacts for chr12. SKIPPING!
[2023-05-11 11:44:34.781] [warning]: read 0 contacts for chr13. SKIPPING!
[2023-05-11 11:44:34.783] [warning]: read 0 contacts for chr14. SKIPPING!
[2023-05-11 11:44:34.785] [warning]: read 0 contacts for chr15. SKIPPING!
[2023-05-11 11:44:34.786] [warning]: read 0 contacts for chr16. SKIPPING!
[2023-05-11 11:44:34.788] [warning]: read 0 contacts for chr17. SKIPPING!
[2023-05-11 11:44:34.789] [warning]: read 0 contacts for chr18. SKIPPING!
[2023-05-11 11:44:34.791] [warning]: read 0 contacts for chr19. SKIPPING!
[2023-05-11 11:44:34.791] [info]: processing contacts for chr20...
[2023-05-11 11:44:35.013] [info]: applying Gaussian blur with sigma=1 to contacts for chr20...
[2023-05-11 11:44:35.029] [info]: chr20 processing took 237.595086ms
[2023-05-11 11:44:35.159] [warning]: read 0 contacts for chr21. SKIPPING!
[2023-05-11 11:44:35.159] [warning]: read 0 contacts for chr22. SKIPPING!
[2023-05-11 11:44:35.159] [warning]: read 0 contacts for chrX. SKIPPING!
[2023-05-11 11:44:35.159] [warning]: read 0 contacts for chrY. SKIPPING!
[2023-05-11 11:44:35.159] [info]: DONE! Processed 24 chromosomes in 402.780193ms!
[2023-05-11 11:44:35.159] [info]: Transformed contacts have been saved to file "/tmp/modle-tools-vew8zaAIaC/out_blurred.cool"
[2023-05-11 11:44:35.283] [info]: transforming contacts from Cooler at URI "modle/test/data/integration_tests/4DNFI9GMP2J8_chr20_25kbp.cool"...
[2023-05-11 11:44:35.289] [warning]: read 0 contacts for chr1. SKIPPING!
[2023-05-11 11:44:35.290] [warning]: read 0 contacts for chr2. SKIPPING!
[2023-05-11 11:44:35.292] [warning]: read 0 contacts for chr3. SKIPPING!
[2023-05-11 11:44:35.294] [warning]: read 0 contacts for chr4. SKIPPING!
[2023-05-11 11:44:35.295] [warning]: read 0 contacts for chr5. SKIPPING!
[2023-05-11 11:44:35.297] [warning]: read 0 contacts for chr6. SKIPPING!
[2023-05-11 11:44:35.298] [warning]: read 0 contacts for chr7. SKIPPING!
[2023-05-11 11:44:35.299] [warning]: read 0 contacts for chr8. SKIPPING!
[2023-05-11 11:44:35.301] [warning]: read 0 contacts for chr9. SKIPPING!
[2023-05-11 11:44:35.303] [warning]: read 0 contacts for chr10. SKIPPING!
[2023-05-11 11:44:35.304] [warning]: read 0 contacts for chr11. SKIPPING!
[2023-05-11 11:44:35.306] [warning]: read 0 contacts for chr12. SKIPPING!
[2023-05-11 11:44:35.308] [warning]: read 0 contacts for chr13. SKIPPING!
[2023-05-11 11:44:35.310] [warning]: read 0 contacts for chr14. SKIPPING!
[2023-05-11 11:44:35.311] [warning]: read 0 contacts for chr15. SKIPPING!
[2023-05-11 11:44:35.312] [warning]: read 0 contacts for chr16. SKIPPING!
[2023-05-11 11:44:35.314] [warning]: read 0 contacts for chr17. SKIPPING!
[2023-05-11 11:44:35.315] [warning]: read 0 contacts for chr18. SKIPPING!
[2023-05-11 11:44:35.317] [warning]: read 0 contacts for chr19. SKIPPING!
[2023-05-11 11:44:35.317] [info]: processing contacts for chr20...
[2023-05-11 11:44:35.540] [info]: computing the difference of Gaussians for chr20 (sigma1=1; sigma2=1.6)...
[2023-05-11 11:44:35.582] [info]: chr20 processing took 265.136791ms
[2023-05-11 11:44:35.687] [warning]: read 0 contacts for chr21. SKIPPING!
[2023-05-11 11:44:35.687] [warning]: read 0 contacts for chr22. SKIPPING!
[2023-05-11 11:44:35.687] [warning]: read 0 contacts for chrX. SKIPPING!
[2023-05-11 11:44:35.687] [warning]: read 0 contacts for chrY. SKIPPING!
[2023-05-11 11:44:35.687] [info]: DONE! Processed 24 chromosomes in 404.878477ms!
[2023-05-11 11:44:35.687] [info]: Transformed contacts have been saved to file "/tmp/modle-tools-vew8zaAIaC/out_dog.cool"
Comparing /tmp/modle-tools-vew8zaAIaC/out_blurred.cool with modle/test/data/integration_tests/4DNFI9GMP2J8_chr20_25kbp_blurred.cool...
Files are identical
Comparing /tmp/modle-tools-vew8zaAIaC/out_dog.cool with modle/test/data/integration_tests/4DNFI9GMP2J8_chr20_25kbp_dog.cool...
Files are identical

### PASS ###


Comparing test/data/integration_tests/mt_annotate_barriers_reference_001.bed.xz with /tmp/modle-tools-6bIboMh8To/out.bed.xz...
Files are identical

### PASS ###

Installation

Once all tests have passed, modle and modle_tools can be installed as follows:

# Activate venv
user@dev:/tmp$ . /tmp/venv/bin/activate

# Install system-wide (requires root/admin rights)
user@dev:/tmp$ cmake --install /tmp/modle/build
-- Install configuration: "Release"
-- Installing: /usr/local/bin/modle_tools
-- Installing: /usr/local/share/licenses/modle_tools/LICENSE
-- Installing: /usr/local/bin/modle
-- Installing: /usr/local/share/licenses/modle/LICENSE

# Alternatively, install to custom path
user@dev:/tmp$ cmake --install /tmp/modle/build --prefix "$HOME/.local/"
-- Install configuration: "Release"
-- Installing: /home/user/.local/bin/modle_tools
-- Installing: /home/user/.local/share/licenses/modle_tools/LICENSE
-- Installing: /home/user/.local/bin/modle
-- Installing: /home/user/.local/share/licenses/modle/LICENSE

Cleaning build artifacts

After successfully compiling MoDLE the following folders safely be removed:

  • Python virtualenv: /tmp/venv
  • MoDLE source tree: /tmp/modle

If you are not using Conan in any other project feel free to also delete Conan's folder ~/.conan2/

Clone this wiki locally