From 3651b4705a5171b2e7eddebdeb32559dd07a68de Mon Sep 17 00:00:00 2001 From: jalil Date: Sun, 25 Aug 2024 22:11:59 +0200 Subject: [PATCH] bug in regression 1 fixed --- runs.ipynb | 864 ++++++++++++++++++ scripts/run_grn_evaluation_tw.sh | 24 +- scripts/run_pc_vs_nc.sh | 86 ++ scripts/run_robust_analys.sh | 27 +- src/methods/multi_omics/scglue/main.py | 2 - src/metrics/regression_1/main.py | 9 +- src/robustness_analysis/script.py | 74 +- src/workflows/run_grn_evaluation/main.nf | 3 +- .../run_robustness_analysis/config.vsh.yaml | 2 +- src/workflows/run_robustness_analysis/main.nf | 6 +- 10 files changed, 1046 insertions(+), 51 deletions(-) create mode 100644 runs.ipynb create mode 100644 scripts/run_pc_vs_nc.sh diff --git a/runs.ipynb b/runs.ipynb new file mode 100644 index 000000000..87a317d0c --- /dev/null +++ b/runs.ipynb @@ -0,0 +1,864 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Robustness analysis" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "temporaryFolder: /tmp/viash_hub_repo6781851242121513146 uri: https://github.com/openproblems-bio/openproblems-v2.git\n", + "Cloning into '.'...\n", + "checkout out: List(git, checkout, origin/main_build, --, .) 0 \n", + "temporaryFolder: /tmp/viash_hub_repo5384776323514779876 uri: https://github.com/openproblems-bio/openproblems-v2.git\n", + "Cloning into '.'...\n", + "checkout out: List(git, checkout, origin/main_build, --, .) 0 \n", + "\u001b[37mExporting positive_control (control_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/control_methods/positive_control\u001b[0m\n", + "\u001b[37mExporting create_component (common) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/common/create_component\u001b[0m\n", + "\u001b[37mExporting create_test_resources (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/create_test_resources\u001b[0m\n", + "\u001b[37mExporting sc_counts (perturbation) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/perturbation/sc_counts\u001b[0m\n", + "\u001b[37mExporting process_perturbation (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/process_perturbation\u001b[0m\n", + "\u001b[37mExporting create_test_data (testdata) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/testdata/create_test_data\u001b[0m\n", + "\u001b[37mExporting regression_2 (metrics) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/metrics/regression_2\u001b[0m\n", + "\u001b[37mExporting noise_grn (robustness_analysis) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/robustness_analysis/noise_grn\u001b[0m\n", + "\u001b[37mExporting explanatory_analysis =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/explanatory_analysis\u001b[0m\n", + "\u001b[37mExporting normalization (perturbation) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/perturbation/normalization\u001b[0m\n", + "\u001b[37mExporting scenicplus (grn_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/grn_methods/scenicplus\u001b[0m\n", + "\u001b[37mExporting batch_correction_seurat (perturbation) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/perturbation/batch_correction_seurat\u001b[0m\n", + "\u001b[37mExporting normalization (perturbation) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/perturbation/normalization\u001b[0m\n", + "\u001b[37mExporting batch_correction_seurat (perturbation) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/perturbation/batch_correction_seurat\u001b[0m\n", + "\u001b[37mExporting celloracle (grn_methods) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/grn_methods/celloracle\u001b[0m\n", + "\u001b[37mExporting explanatory_analysis =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/explanatory_analysis\u001b[0m\n", + "\u001b[37mExporting sc_counts (perturbation) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/perturbation/sc_counts\u001b[0m\n", + "\u001b[37mExporting create_test_data (testdata) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/testdata/create_test_data\u001b[0m\n", + "\u001b[37mExporting sc_counts (perturbation) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/perturbation/sc_counts\u001b[0m\n", + "\u001b[37mExporting celloracle (grn_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/grn_methods/celloracle\u001b[0m\n", + "\u001b[37mExporting granie (grn_methods) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/grn_methods/granie\u001b[0m\n", + "\u001b[37mExporting dummy (grn_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/grn_methods/dummy\u001b[0m\n", + "\u001b[37mExporting run_grn_evaluation (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/run_grn_evaluation\u001b[0m\n", + "\u001b[37mExporting process_multiomics (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/process_multiomics\u001b[0m\n", + "\u001b[37mExporting grn_inference_scenicplus (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/grn_inference_scenicplus\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/control_methods/positive_control:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/robustness_analysis/noise_grn:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/perturbation/normalization:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/explanatory_analysis:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting format_data (multiomics) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/multiomics/format_data\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/common/create_component:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting create_test_data (testdata) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/testdata/create_test_data\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/perturbation/sc_counts:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting noise_grn (robustness_analysis) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/robustness_analysis/noise_grn\u001b[0m\n", + "\u001b[37mExporting granie (grn_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/grn_methods/granie\u001b[0m\n", + "\u001b[37mExporting scglue (grn_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/grn_methods/scglue\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/grn_methods/dummy:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting grn_inference_celloracle (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/grn_inference_celloracle\u001b[0m\n", + "\u001b[37mExporting run_robustness_analysis (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/run_robustness_analysis\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/multiomics/format_data:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/testdata/create_test_data:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting grn_inference_granie (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/grn_inference_granie\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/grn_methods/scglue:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting granie (grn_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/grn_methods/granie\u001b[0m\n", + "\u001b[37mExporting explanatory_analysis =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/explanatory_analysis\u001b[0m\n", + "\u001b[37mExporting multiome_matrix (multiomics) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/multiomics/multiome_matrix\u001b[0m\n", + "\u001b[37mExporting scenicplus (grn_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/grn_methods/scenicplus\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/grn_methods/granie:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting multiome_matrix (multiomics) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/multiomics/multiome_matrix\u001b[0m\n", + "\u001b[37mExporting positive_control (control_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/control_methods/positive_control\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/grn_methods/scenicplus:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting batch_correction_evaluation (perturbation) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/perturbation/batch_correction_evaluation\u001b[0m\n", + "\u001b[37mExporting format_resources_r (multiomics) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/multiomics/format_resources_r\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/multiomics/format_resources_r:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/perturbation/batch_correction_evaluation:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting dummy (grn_methods) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/grn_methods/dummy\u001b[0m\n", + "\u001b[37mExporting dummy (grn_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/grn_methods/dummy\u001b[0m\n", + "\u001b[37mExporting celloracle (grn_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/grn_methods/celloracle\u001b[0m\n", + "\u001b[37mExporting create_component (common) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/common/create_component\u001b[0m\n", + "\u001b[37mExporting create_component (common) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/common/create_component\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/grn_methods/celloracle:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting normalization (perturbation) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/perturbation/normalization\u001b[0m\n", + "\u001b[37mExporting sync_test_resources (common) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/common/sync_test_resources\u001b[0m\n", + "\u001b[37mExporting sync_test_resources (common) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/common/sync_test_resources\u001b[0m\n", + "\u001b[37mExporting sync_test_resources (common) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/common/sync_test_resources\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/common/sync_test_resources:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting negative_control (control_methods) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/control_methods/negative_control\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/control_methods/negative_control:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting format_data (multiomics) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/multiomics/format_data\u001b[0m\n", + "\u001b[37mExporting scglue (grn_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/grn_methods/scglue\u001b[0m\n", + "\u001b[37mExporting format_data (multiomics) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/multiomics/format_data\u001b[0m\n", + "\u001b[37mExporting grn_inference_scglue (workflows) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/workflows/grn_inference_scglue\u001b[0m\n", + "\u001b[37mExporting batch_correction_evaluation (perturbation) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/perturbation/batch_correction_evaluation\u001b[0m\n", + "\u001b[37mExporting format_resources_r (multiomics) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/multiomics/format_resources_r\u001b[0m\n", + "\u001b[37mExporting regression_1 (metrics) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/metrics/regression_1\u001b[0m\n", + "\u001b[37mExporting batch_correction_scgen (perturbation) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/perturbation/batch_correction_scgen\u001b[0m\n", + "\u001b[37mExporting multiome_matrix (multiomics) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/multiomics/multiome_matrix\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/perturbation/batch_correction_scgen:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/metrics/regression_1:dev' with Dockerfile\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/multiomics/multiome_matrix:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting format_resources_r (multiomics) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/multiomics/format_resources_r\u001b[0m\n", + "\u001b[37mExporting batch_correction_scgen (perturbation) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/perturbation/batch_correction_scgen\u001b[0m\n", + "\u001b[37mExporting batch_correction_scgen (perturbation) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/perturbation/batch_correction_scgen\u001b[0m\n", + "\u001b[37mExporting batch_correction_seurat (perturbation) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/perturbation/batch_correction_seurat\u001b[0m\n", + "\u001b[37mExporting scenicplus (grn_methods) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/grn_methods/scenicplus\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/perturbation/batch_correction_seurat:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting batch_correction_evaluation (perturbation) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/perturbation/batch_correction_evaluation\u001b[0m\n", + "\u001b[37mExporting negative_control (control_methods) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/control_methods/negative_control\u001b[0m\n", + "\u001b[37mExporting regression_1 (metrics) =nextflow=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/nextflow/metrics/regression_1\u001b[0m\n", + "\u001b[37mExporting regression_2 (metrics) =docker=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/docker/metrics/regression_2\u001b[0m\n", + "\u001b[37m[notice] Building container 'ghcr.io/openproblems-bio/task_grn_inference/metrics/regression_2:dev' with Dockerfile\u001b[0m\n", + "\u001b[37mExporting scglue (grn_methods) =native=> /mnt/c/Users/nourisa/Documents/testProjs/ongoing/task_grn_benchmark/target/native/grn_methods/scglue\u001b[0m\n", + "\u001b[32mAll 70 configs built successfully\u001b[0m\n" + ] + } + ], + "source": [ + "!viash ns build --setup cb --parallel" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "[Errno 2] Unable to synchronously open file (unable to open file: name = 'resources/gen-benchmark/perturbation_data.h5ad', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[11], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01manndata\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mad\u001b[39;00m \n\u001b[0;32m----> 2\u001b[0m \u001b[43mad\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mread_h5ad\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mresources/gen-benchmark/perturbation_data.h5ad\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/anndata/_io/h5ad.py:237\u001b[0m, in \u001b[0;36mread_h5ad\u001b[0;34m(filename, backed, as_sparse, as_sparse_fmt, chunk_size)\u001b[0m\n\u001b[1;32m 229\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mNotImplementedError\u001b[39;00m(\n\u001b[1;32m 230\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCurrently only `X` and `raw/X` can be read as sparse.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 231\u001b[0m )\n\u001b[1;32m 233\u001b[0m rdasp \u001b[38;5;241m=\u001b[39m partial(\n\u001b[1;32m 234\u001b[0m read_dense_as_sparse, sparse_format\u001b[38;5;241m=\u001b[39mas_sparse_fmt, axis_chunk\u001b[38;5;241m=\u001b[39mchunk_size\n\u001b[1;32m 235\u001b[0m )\n\u001b[0;32m--> 237\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[43mh5py\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFile\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mr\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m f:\n\u001b[1;32m 239\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcallback\u001b[39m(func, elem_name: \u001b[38;5;28mstr\u001b[39m, elem, iospec):\n\u001b[1;32m 240\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m iospec\u001b[38;5;241m.\u001b[39mencoding_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124manndata\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mor\u001b[39;00m elem_name\u001b[38;5;241m.\u001b[39mendswith(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/h5py/_hl/files.py:562\u001b[0m, in \u001b[0;36mFile.__init__\u001b[0;34m(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, meta_block_size, **kwds)\u001b[0m\n\u001b[1;32m 553\u001b[0m fapl \u001b[38;5;241m=\u001b[39m make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,\n\u001b[1;32m 554\u001b[0m locking, page_buf_size, min_meta_keep, min_raw_keep,\n\u001b[1;32m 555\u001b[0m alignment_threshold\u001b[38;5;241m=\u001b[39malignment_threshold,\n\u001b[1;32m 556\u001b[0m alignment_interval\u001b[38;5;241m=\u001b[39malignment_interval,\n\u001b[1;32m 557\u001b[0m meta_block_size\u001b[38;5;241m=\u001b[39mmeta_block_size,\n\u001b[1;32m 558\u001b[0m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwds)\n\u001b[1;32m 559\u001b[0m fcpl \u001b[38;5;241m=\u001b[39m make_fcpl(track_order\u001b[38;5;241m=\u001b[39mtrack_order, fs_strategy\u001b[38;5;241m=\u001b[39mfs_strategy,\n\u001b[1;32m 560\u001b[0m fs_persist\u001b[38;5;241m=\u001b[39mfs_persist, fs_threshold\u001b[38;5;241m=\u001b[39mfs_threshold,\n\u001b[1;32m 561\u001b[0m fs_page_size\u001b[38;5;241m=\u001b[39mfs_page_size)\n\u001b[0;32m--> 562\u001b[0m fid \u001b[38;5;241m=\u001b[39m \u001b[43mmake_fid\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mmode\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43muserblock_size\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfapl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfcpl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mswmr\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mswmr\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 564\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(libver, \u001b[38;5;28mtuple\u001b[39m):\n\u001b[1;32m 565\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_libver \u001b[38;5;241m=\u001b[39m libver\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/h5py/_hl/files.py:235\u001b[0m, in \u001b[0;36mmake_fid\u001b[0;34m(name, mode, userblock_size, fapl, fcpl, swmr)\u001b[0m\n\u001b[1;32m 233\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m swmr \u001b[38;5;129;01mand\u001b[39;00m swmr_support:\n\u001b[1;32m 234\u001b[0m flags \u001b[38;5;241m|\u001b[39m\u001b[38;5;241m=\u001b[39m h5f\u001b[38;5;241m.\u001b[39mACC_SWMR_READ\n\u001b[0;32m--> 235\u001b[0m fid \u001b[38;5;241m=\u001b[39m \u001b[43mh5f\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mflags\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfapl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfapl\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 236\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m mode \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mr+\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[1;32m 237\u001b[0m fid \u001b[38;5;241m=\u001b[39m h5f\u001b[38;5;241m.\u001b[39mopen(name, h5f\u001b[38;5;241m.\u001b[39mACC_RDWR, fapl\u001b[38;5;241m=\u001b[39mfapl)\n", + "File \u001b[0;32mh5py/_objects.pyx:54\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32mh5py/_objects.pyx:55\u001b[0m, in \u001b[0;36mh5py._objects.with_phil.wrapper\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32mh5py/h5f.pyx:102\u001b[0m, in \u001b[0;36mh5py.h5f.open\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] Unable to synchronously open file (unable to open file: name = 'resources/gen-benchmark/perturbation_data.h5ad', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)" + ] + } + ], + "source": [ + "import anndata as ad \n", + "ad.read_h5ad('resources/gen-benchmark/perturbation_data.h5ad')" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "net\n", + "\u001b[33mNextflow 24.04.4 is available - Please consider updating your version to it\u001b[m\n", + "N E X T F L O W ~ version 23.10.4\n", + "Launching `target/nextflow/workflows/run_robustness_analysis/main.nf` [scruffy_aryabhata] DSL2 - revision: 5b136b3396\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "\u001b[2A\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", 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[ 0%] 0 of 19\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[6A\n", + "executor > local (27)\u001b[K\n", + "[b1/8fd36e] process > run_robustness_analysis:run... [ 87%] 21 of 24\u001b[K\n", + "[44/9481b7] process > run_robustness_analysis:run... [ 0%] 0 of 20\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[6A\n", + "executor > local (27)\u001b[K\n", + "[b1/8fd36e] process > run_robustness_analysis:run... [ 87%] 21 of 24\u001b[K\n", + "[44/9481b7] process > run_robustness_analysis:run... [ 0%] 0 of 21\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[6A\n", + "executor > local (28)\u001b[K\n", + "[a6/8c9eba] process > run_robustness_analysis:run... [ 91%] 22 of 24\u001b[K\n", + "[df/316561] process > run_robustness_analysis:run... [ 0%] 0 of 22\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[6A\n", + "executor > local (29)\u001b[K\n", + "[18/2e36a1] process > run_robustness_analysis:run... [ 95%] 23 of 24\u001b[K\n", + "[c0/1ecdc0] process > run_robustness_analysis:run... [ 0%] 0 of 23\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[6A\n", + "executor > local (30)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[4d/a2a11b] process > run_robustness_analysis:run... [ 0%] 0 of 24\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[6A\n", + "executor > local (31)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[d7/210367] process > run_robustness_analysis:run... [ 4%] 1 of 24, failed: 1\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[7A\n", + "executor > local (31)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[d7/210367] process > run_robustness_analysis:run... [ 4%] 1 of 24, failed: 1\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[7A\n", + "executor > local (32)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[d4/ab7b82] process > run_robustness_analysis:run... [ 8%] 2 of 24, failed: 2\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[66/0f58ee] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[8A\n", + "executor > local (33)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[54/57165c] process > run_robustness_analysis:run... [ 12%] 3 of 24, failed: 3\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[66/0f58ee] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[44/9481b7] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[9A\n", + "executor > local (34)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[58/9c6ddf] process > run_robustness_analysis:run... [ 16%] 4 of 24, failed: 4\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[66/0f58ee] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[44/9481b7] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[10A\n", + "executor > local (35)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[e8/17cc79] process > run_robustness_analysis:run... [ 20%] 5 of 24, failed: 5\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[66/0f58ee] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[44/9481b7] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[11A\n", + "executor > local (36)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[cb/e2f342] process > run_robustness_analysis:run... [ 25%] 6 of 24, failed: 6\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[3b/44ccc6] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[66/0f58ee] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[44/9481b7] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[12A\n", + "executor > local (37)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[84/27b545] process > run_robustness_analysis:run... [ 29%] 7 of 24, failed: 7\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[44/9481b7] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[13A\n", + "executor > local (38)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[b6/b32d77] process > run_robustness_analysis:run... [ 33%] 8 of 24, failed: 8\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[13A\n", + "executor > local (38)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[b6/b32d77] process > run_robustness_analysis:run... [ 33%] 8 of 24, failed: 8\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[12A\n", + "executor > local (39)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[79/be762c] process > run_robustness_analysis:run... [ 37%] 9 of 24, failed: 9\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[df/316561] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[12A\n", + "executor > local (39)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[79/be762c] process > run_robustness_analysis:run... [ 37%] 9 of 24, failed: 9\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[c0/1ecdc0] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[12A\n", + "executor > local (40)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[ab/96bccc] process > run_robustness_analysis:run... [ 41%] 10 of 24, failed: 10\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[4d/a2a11b] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[12A\n", + "executor > local (40)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[ab/96bccc] process > run_robustness_analysis:run... [ 41%] 10 of 24, failed: 10\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[12A\n", + "executor > local (42)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[ed/ad07ab] process > run_robustness_analysis:run... [ 50%] 12 of 24, failed: 12\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[cb/e2f342] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[12A\n", + "executor > local (42)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[ed/ad07ab] process > run_robustness_analysis:run... [ 50%] 12 of 24, failed: 12\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[cb/e2f342] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[12A\n", + "executor > local (43)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[18/d57637] process > run_robustness_analysis:run... [ 54%] 13 of 24, failed: 13\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[d7/210367] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[cb/e2f342] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[13A\n", + "executor > local (44)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[68/e914c5] process > run_robustness_analysis:run... [ 58%] 14 of 24, failed: 14\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[cb/e2f342] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[14A\n", + "executor > local (44)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[68/e914c5] process > run_robustness_analysis:run... [ 58%] 14 of 24, failed: 14\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[d4/ab7b82] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_20.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[54/57165c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[cb/e2f342] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[14A\n", + "executor > local (45)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[2a/ec6bb4] process > run_robustness_analysis:run... [ 62%] 15 of 24, failed: 15\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[58/9c6ddf] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[e8/17cc79] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[cb/e2f342] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[14A\n", + "executor > local (46)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[6c/70d06d] process > run_robustness_analysis:run... [ 66%] 16 of 24, failed: 16\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[14A\n", + "executor > local (46)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[ab/96bccc] process > run_robustness_analysis:run... [ 70%] 17 of 24, failed: 17\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[13A\n", + "executor > local (47)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[89/a9de4a] process > run_robustness_analysis:run... [ 70%] 17 of 24, failed: 17\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[11A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[57/2950fa] process > run_robustness_analysis:run... [ 75%] 18 of 24, failed: 18\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[12A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[57/2950fa] process > run_robustness_analysis:run... [ 75%] 18 of 24, failed: 18\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[13A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[18/d57637] process > run_robustness_analysis:run... [ 79%] 19 of 24, failed: 19\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[13A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[68/e914c5] process > run_robustness_analysis:run... [ 83%] 20 of 24, failed: 20\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[84/27b545] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[b6/b32d77] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[68/e914c5] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[14A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[2a/ec6bb4] process > run_robustness_analysis:run... [ 87%] 21 of 24, failed: 21\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[68/e914c5] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[2a/ec6bb4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[K\n", + "\u001b[15A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[2a/ec6bb4] process > run_robustness_analysis:run... [ 87%] 21 of 24, failed: 21\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[79/be762c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[68/e914c5] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[2a/ec6bb4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[6c/70d06d] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[15A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[89/a9de4a] process > run_robustness_analysis:run... [ 95%] 23 of 24, failed: 23\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[68/e914c5] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[2a/ec6bb4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[6c/70d06d] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[89/a9de4a] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[K\n", + "\u001b[15A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[57/2950fa] process > run_robustness_analysis:run... [100%] 24 of 24, failed:...\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[68/e914c5] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[2a/ec6bb4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[6c/70d06d] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[89/a9de4a] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[57/2950fa] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[15A\n", + "executor > local (48)\u001b[K\n", + "[d2/f3d3bb] process > run_robustness_analysis:run... [100%] 24 of 24 ✔\u001b[K\n", + "[57/2950fa] process > run_robustness_analysis:run... [100%] 24 of 24, failed:...\u001b[K\n", + "[- ] process > run_robustness_analysis:run... -\u001b[K\n", + "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", + "\u001b[33m[c5/ef2c2c] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (granie_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ab/96bccc] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[ed/ad07ab] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_10.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[18/d57637] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scenicplus_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[68/e914c5] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (figr_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[2a/ec6bb4] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_50.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[6c/70d06d] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (collectri_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[89/a9de4a] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (scglue_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[33m[57/2950fa] NOTE: Process `run_robustness_analysis:run_wf:runEachWf:regression_1:processWf:regression_1_process (celloracle_100.regression_1)` terminated with an error exit status (1) -- Error is ignored\u001b[39m\u001b[K\n", + "\u001b[32;1mCompleted at: 25-Aug-2024 20:26:38\n", + "Duration : 3m 9s\n", + "CPU hours : 0.5 (87.7% failed)\n", + "Succeeded : 24\n", + "Ignored : 24\n", + "Failed : 24\n", + "\u001b[22;39m\u001b[K\n", + "\n" + ] + } + ], + "source": [ + "!bash scripts/run_robust_analys.sh \"net\"" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "ename": "FileNotFoundError", + "evalue": "[Errno 2] No such file or directory: '../../task_grn_benchmark/output/robust_analy_net/scores.yaml'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[12], line 5\u001b[0m\n\u001b[1;32m 2\u001b[0m base_folder \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m../../task_grn_benchmark/output/robust_analy_net\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 4\u001b[0m result_file \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mbase_folder\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m/scores.yaml\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m----> 5\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28;43mopen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mresult_file\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mr\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m file:\n\u001b[1;32m 6\u001b[0m data \u001b[38;5;241m=\u001b[39m yaml\u001b[38;5;241m.\u001b[39msafe_load(file)\n\u001b[1;32m 7\u001b[0m df_reg1 \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame({}, columns\u001b[38;5;241m=\u001b[39mgrn_models)\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/IPython/core/interactiveshell.py:324\u001b[0m, in \u001b[0;36m_modified_open\u001b[0;34m(file, *args, **kwargs)\u001b[0m\n\u001b[1;32m 317\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m file \u001b[38;5;129;01min\u001b[39;00m {\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m2\u001b[39m}:\n\u001b[1;32m 318\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 319\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIPython won\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt let you open fd=\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mfile\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m by default \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 320\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mas it is likely to crash IPython. If you know what you are doing, \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 321\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124myou can use builtins\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m open.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 322\u001b[0m )\n\u001b[0;32m--> 324\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mio_open\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", + "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '../../task_grn_benchmark/output/robust_analy_net/scores.yaml'" + ] + } + ], + "source": [ + "# base_folder = '../../task_grn_benchmark/resources/results/robust_analy_links'\n", + "base_folder = '../../task_grn_benchmark/output/robust_analy_net'\n", + "\n", + "result_file = f'{base_folder}/scores.yaml'\n", + "with open(result_file, 'r') as file:\n", + " data = yaml.safe_load(file)\n", + "df_reg1 = pd.DataFrame({}, columns=grn_models)\n", + "# Iterate over the data\n", + "for entry in data:\n", + " method_id = entry['method_id']\n", + " reg_type, degree, method = method_id.split('-')\n", + " if reg_type == 'reg1':\n", + " col = 'ex(True)_tf(-1)'\n", + " ex_true_tf_idx = entry['metric_ids'].index(col)\n", + " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n", + " df_reg1.loc[int(degree), method] = ex_true_tf_value\n", + "\n", + "df_reg1.sort_index()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "fig, axes = plt.subplots(1, 2, figsize=(5,3), sharey=True)\n", + "df_reg1.index = df_reg1.index.map(surragate_names)\n", + "df_reg1.columns = df_reg1.columns.map(surragate_names)\n", + "\n", + "ax = axes[0]\n", + "headmap(df_reg1, name='', ax=ax, fmt='.03f')\n", + "ax.xaxis.set_label_position('top')\n", + "ax.xaxis.tick_top()\n", + "ax.set_xticklabels(ax.get_xticklabels(), rotation=45, ha='left')\n", + "\n", + "# ax = axes[1]\n", + "# scores_rank = scores_mat.rank(ascending=False)\n", + "# scores_rank['Mean'] = scores_rank.mean(axis=1)\n", + "# headmap_rank(scores_rank, name='', ax=ax)\n", + "# ax.xaxis.set_label_position('top')\n", + "# ax.xaxis.tick_top()\n", + "# ax.set_xticklabels(ax.get_xticklabels(), rotation=45, ha='left')\n", + "\n", + "# plt.savefig(f'{results_folder}/benchmark/figs/final-reg2.png', dpi=300, transparent=True, bbox_inches='tight')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "py10", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.14" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/scripts/run_grn_evaluation_tw.sh b/scripts/run_grn_evaluation_tw.sh index c65bb8908..ed52929b8 100644 --- a/scripts/run_grn_evaluation_tw.sh +++ b/scripts/run_grn_evaluation_tw.sh @@ -1,15 +1,13 @@ #!/bin/bash # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" - -RUN_ID="pearson_gb" +RUN_ID="pearson_gb_subsample" resources_dir="s3://openproblems-data/resources/grn" publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}" -# grn_models_folder="${resources_dir}/supplementary/grn_models_noised" grn_models_folder="${resources_dir}/grn_models" reg_type=GB subsample=-2 -max_workers=20 +max_workers=10 param_file="./params/${RUN_ID}.yaml" @@ -77,14 +75,14 @@ HERE # -c src/common/nextflow_helpers/labels_ci.config \ # -params-file ${param_file} -./tw-windows-x86_64.exe launch ` - https://github.com/openproblems-bio/task_grn_benchmark.git ` - --revision build/main ` - --pull-latest ` - --main-script target/nextflow/workflows/run_grn_evaluation/main.nf ` - --workspace 53907369739130 ` - --compute-env 6TeIFgV5OY4pJCk8I0bfOh ` - --params-file ./params/scgen_pearson_gb_pcs.yaml ` - --config src/common/nextflow_helpers/labels_tw.config +# ./tw-windows-x86_64.exe launch ` +# https://github.com/openproblems-bio/task_grn_benchmark.git ` +# --revision build/main ` +# --pull-latest ` +# --main-script target/nextflow/workflows/run_grn_evaluation/main.nf ` +# --workspace 53907369739130 ` +# --compute-env 6TeIFgV5OY4pJCk8I0bfOh ` +# --params-file ./params/scgen_pearson_gb_pcs.yaml ` +# --config src/common/nextflow_helpers/labels_tw.config diff --git a/scripts/run_pc_vs_nc.sh b/scripts/run_pc_vs_nc.sh new file mode 100644 index 000000000..52e851695 --- /dev/null +++ b/scripts/run_pc_vs_nc.sh @@ -0,0 +1,86 @@ +#!/bin/bash + +# RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" + +subsamples=(-2 -3 -4) + +RUN_ID="robust_analy_$1" +resources_dir="resources" +publish_dir="output/${RUN_ID}" + +# resources_dir="s3://openproblems-data/resources/grn" +# publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}" + +grn_models_folder="${resources_dir}/grn_models" + + +reg_type=ridge +max_workers=10 +layer=pearson + +param_file="./params/${RUN_ID}.yaml" + +grn_names=( + "collectri" + "celloracle" + "scenicplus" + "figr" + "granie" + "scglue" +) + + + +# Start writing to the YAML file +cat > $param_file << HERE +param_list: +HERE + +append_entry() { + cat >> $param_file << HERE + - id: ${1}_${2} + perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad + layer: ${layer} + reg_type: $reg_type + method_id: ${2}-${1} + subsample: $2 + max_workers: $max_workers + consensus: ${resources_dir}/prior/consensus-num-regulators.json + prediction: ${grn_models_folder}/$1.csv + degree: 0 + +HERE +} +# Loop through grn_names and layers +for subsample in "${subsamples[@]}"; do + for grn_name in "${grn_names[@]}"; do + append_entry "$grn_name" "$subsample" + done +done + + + +# Append the remaining output_state and publish_dir to the YAML file +cat >> $param_file << HERE +output_state: "state.yaml" +publish_dir: "$publish_dir" +HERE + +nextflow run . \ + -main-script target/nextflow/workflows/run_robustness_analysis/main.nf \ + -profile docker \ + -with-trace \ + -c src/common/nextflow_helpers/labels_ci.config \ + -params-file ${param_file} + +# ./tw-windows-x86_64.exe launch ` +# https://github.com/openproblems-bio/task_grn_benchmark.git ` +# --revision build/main ` +# --pull-latest ` +# --main-script target/nextflow/workflows/run_grn_evaluation/main.nf ` +# --workspace 53907369739130 ` +# --compute-env 6TeIFgV5OY4pJCk8I0bfOh ` +# --params-file ./params/scgen_pearson_gb_pcs.yaml ` +# --config src/common/nextflow_helpers/labels_tw.config + + diff --git a/scripts/run_robust_analys.sh b/scripts/run_robust_analys.sh index 876e06f5f..6d95347a3 100644 --- a/scripts/run_robust_analys.sh +++ b/scripts/run_robust_analys.sh @@ -2,7 +2,11 @@ # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" -RUN_ID="robust_analy" +degrees=(0 10 20 50 100) +noise_type="$1" +echo $noise_type + +RUN_ID="robust_analy_$1" resources_dir="resources" publish_dir="output/${RUN_ID}" @@ -19,7 +23,6 @@ layer=pearson param_file="./params/${RUN_ID}.yaml" - grn_names=( "collectri" "celloracle" @@ -29,8 +32,7 @@ grn_names=( "scglue" ) -degrees=(10 20 50 100) -types=(links weight) + # Start writing to the YAML file cat > $param_file << HERE @@ -39,28 +41,27 @@ HERE append_entry() { cat >> $param_file << HERE - - id: ${1}_${2}_${3} + - id: ${1}_${2} perturbation_data: ${resources_dir}/grn-benchmark/perturbation_data.h5ad layer: ${layer} reg_type: $reg_type - method_id: $1 + method_id: ${2}-${1} subsample: $subsample max_workers: $max_workers consensus: ${resources_dir}/prior/consensus-num-regulators.json prediction: ${grn_models_folder}/$1.csv - degree: ${3} - type: ${2} + degree: ${2} + noise_type: ${noise_type} HERE } # Loop through grn_names and layers -for type in "${types[@]}"; do - for degree in "${degrees[@]}"; do - for grn_name in "${grn_names[@]}"; do - append_entry "$grn_name" "$type" "$degree" - done +for degree in "${degrees[@]}"; do + for grn_name in "${grn_names[@]}"; do + append_entry "$grn_name" "$degree" done done + # Append the remaining output_state and publish_dir to the YAML file cat >> $param_file << HERE output_state: "state.yaml" diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py index e2f2ddf42..7e6ac4ac9 100644 --- a/src/methods/multi_omics/scglue/main.py +++ b/src/methods/multi_omics/scglue/main.py @@ -27,8 +27,6 @@ def preprocess(rna, atac, par): sc.pp.neighbors(atac, use_rep="X_lsi", metric="cosine") sc.tl.umap(atac) print('step 2 completed') - - scglue.data.get_gene_annotation( rna, gtf=par['annotation_file'], diff --git a/src/metrics/regression_1/main.py b/src/metrics/regression_1/main.py index 2e5d4dbc4..3b0b6817d 100644 --- a/src/metrics/regression_1/main.py +++ b/src/metrics/regression_1/main.py @@ -181,8 +181,6 @@ def main(par): reg_type = par['reg_type'] max_workers = par['max_workers'] layer = par["layer"] - pert_df = pd.DataFrame(perturbation_data.layers[layer], columns=gene_names) - if subsample == -1: pass elif subsample == -2: # one combination of cell_type, sm_name @@ -192,11 +190,18 @@ def main(par): for _, row in obs.iterrows(): mask.append((sampled_obs==row).all(axis=1).any()) perturbation_data = perturbation_data[mask,:] + elif subsample == -3: #negative control + mask = perturbation_data.obs.sm_name == 'Dimethyl Sulfoxide' + perturbation_data = perturbation_data[mask,:] + elif subsample == -4: #positive control + mask = perturbation_data.obs.sm_name.isin(['Dabrafenib', 'Belinostat']) + perturbation_data = perturbation_data[mask,:] else: perturbation_data = perturbation_data[np.random.choice(perturbation_data.n_obs, subsample, replace=False), :] print(perturbation_data.shape) + pert_df = pd.DataFrame(perturbation_data.layers[layer], columns=gene_names) pert_df = pert_df.T # make it gene*sample # process net diff --git a/src/robustness_analysis/script.py b/src/robustness_analysis/script.py index 68efe5daa..407ed7232 100644 --- a/src/robustness_analysis/script.py +++ b/src/robustness_analysis/script.py @@ -7,28 +7,74 @@ "prediction": "resources/grn_models/collectri.csv", "prediction_n": "output/grn_noised.csv", 'degree': 20, - 'type': 'links' + 'noise_type': 'links' } ## VIASH END degree = par['degree']/100 +type = par['noise_type'] + prediction = pd.read_csv(par['prediction']) -assert 'weight' in prediction.columns - -if type =='weight': - print('Add noise to weight') - std_dev = prediction['weight'].std() - noise = np.random.normal(0, degree * std_dev, size=prediction['weight'].shape) - prediction['weight'] += noise - -elif type =='links': - print('Permute links') - num_rows_to_permute = int(len(prediction) * degree) - permute_indices = np.random.choice(prediction.index, size=num_rows_to_permute, replace=False) + + +if type == 'weight': # add noise to weight + assert 'weight' in prediction.columns + print('Add noise to weight') + std_dev = prediction['weight'].std() + noise = np.random.normal(0, degree * std_dev, size=prediction['weight'].shape) + prediction['weight'] += noise + +elif type == 'links': # shuffle source-target-weight + print('Permute links') + num_rows_to_permute = int(len(prediction) * degree) + permute_indices = np.random.choice(prediction.index, size=num_rows_to_permute, replace=False) + prediction.loc[permute_indices, 'weight'] = np.random.permutation(prediction.loc[permute_indices, 'weight'].values) + +elif type == 'net': # shuffle source-target matrix + print('Permute links') - prediction.loc[permute_indices, 'weight'] = np.random.permutation(prediction.loc[permute_indices, 'weight'].values) + # 1. Pivot the GRN with target as index and source as columns + pivot_df = prediction.pivot(index='target', columns='source', values='weight') + + # Fill NaNs with 0 or a value of your choice + pivot_df.fillna(0, inplace=True) + + # 2. Randomly choose 20% of the matrix to shuffle + matrix_flattened = pivot_df.values.flatten() + n_elements = len(matrix_flattened) + n_shuffle = int(n_elements * degree) + + # Randomly select 20% of the matrix elements' indices + shuffle_indices = np.random.choice(n_elements, n_shuffle, replace=False) + + # Get the values that will be shuffled + shuffle_values = matrix_flattened[shuffle_indices] + + # 3. Shuffle the selected values + np.random.shuffle(shuffle_values) + + # Assign the shuffled values back to the selected positions + matrix_flattened[shuffle_indices] = shuffle_values + + # Reshape the flattened array back into the matrix + pivot_df_shuffled = pd.DataFrame(matrix_flattened.reshape(pivot_df.shape), + index=pivot_df.index, + columns=pivot_df.columns) + + flat_df = pivot_df_shuffled.reset_index() + + # Melt the DataFrame to turn it back into long-form (source-target-weight) + prediction = flat_df.melt(id_vars='target', var_name='source', value_name='weight') + + + prediction = prediction[prediction['weight'] !=0 ].reset_index(drop=True) + + +else: + raise ValueError(f'Wrong type ({type}) for adding noise') + print('Output noised GRN') prediction.to_csv(par['prediction_n']) diff --git a/src/workflows/run_grn_evaluation/main.nf b/src/workflows/run_grn_evaluation/main.nf index 12cbc7f93..d3eb8ee16 100644 --- a/src/workflows/run_grn_evaluation/main.nf +++ b/src/workflows/run_grn_evaluation/main.nf @@ -14,8 +14,7 @@ workflow run_wf { // construct list of metrics metrics = [ - regression_1, - regression_2 + regression_1 ] /*************************** diff --git a/src/workflows/run_robustness_analysis/config.vsh.yaml b/src/workflows/run_robustness_analysis/config.vsh.yaml index 338a90348..ea8da0aef 100644 --- a/src/workflows/run_robustness_analysis/config.vsh.yaml +++ b/src/workflows/run_robustness_analysis/config.vsh.yaml @@ -44,7 +44,7 @@ functionality: required: false direction: input default: 20 - - name: --type + - name: --noise_type type: string required: false direction: input diff --git a/src/workflows/run_robustness_analysis/main.nf b/src/workflows/run_robustness_analysis/main.nf index feca5f6f0..a78e02f3d 100644 --- a/src/workflows/run_robustness_analysis/main.nf +++ b/src/workflows/run_robustness_analysis/main.nf @@ -27,7 +27,7 @@ workflow run_wf { | noise_grn.run( fromState: [ - prediction: "prediction" + prediction: "prediction", degree: "degree", noise_type: "noise_type" ], toState: [ prediction_n: "prediction_n" @@ -49,9 +49,7 @@ workflow run_wf { reg_type: "reg_type", method_id: "method_id", max_workers: "max_workers", - consensus: "consensus", - degree: "degree", - type: "type" + consensus: "consensus" ], // use 'toState' to publish that component's outputs to the overall state toState: { id, output, state, comp ->