From 741a02bc60e7bd7e6f87a996a23ab76f33f5a496 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 28 Jun 2024 12:29:11 +0200 Subject: [PATCH] Removing temporal test reports wrongly uploaded --- tool_test_output.html | 291 ---------------------------------- tool_test_output.json | 101 ------------ tools/biobb_pytorch/.DS_Store | Bin 6148 -> 0 bytes 3 files changed, 392 deletions(-) delete mode 100644 tool_test_output.html delete mode 100644 tool_test_output.json delete mode 100644 tools/biobb_pytorch/.DS_Store diff --git a/tool_test_output.html b/tool_test_output.html deleted file mode 100644 index 6c774a2c..00000000 --- a/tool_test_output.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - - Test Results (powered by Planemo) - - - - - - - - - - -
-
-
-
- - - - - - - \ No newline at end of file diff --git a/tool_test_output.json b/tool_test_output.json deleted file mode 100644 index c0501a12..00000000 --- a/tool_test_output.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "summary": { - "num_errors": 0, - "num_failures": 0, - "num_skips": 0, - "num_tests": 1 - }, - "tests": [ - { - "data": { - "inputs": { - "config_json": { - "id": "8638ae59da399d18", - "src": "hda" - }, - "input_train_npy_path": { - "id": "52e55242f7275d02", - "src": "hda" - }, - "outname_output_model_pth_path": "output_model.pth", - "outname_output_performance_npz_path": "output_performance.npz", - "outname_output_train_data_npz_path": "output_train_data.npz" - }, - "job": { - "command_line": "ln -s /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/files/2/4/5/dataset_245bf14d-1659-4578-a68b-afb1ce9308f1.dat ./input_train_npy_path.npy; ln -s /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/files/2/4/9/dataset_249a96e0-a3d5-42bd-8d9f-8aeb075051f2.dat ./config_json.json; train_mdae --config ./config_json.json --input_train_npy_path ./input_train_npy_path.npy --output_model_pth_path output_model.pth --output_train_data_npz_path output_train_data.npz --output_performance_npz_path output_performance.npz ; mv output_model.pth /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/outputs/dataset_d4a02c99-cb7c-4e22-a5bb-da3d294518d4.dat; if test -f output_train_data.npz; then mv output_train_data.npz /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/outputs/dataset_c853af5a-bc40-41fe-8d2f-8380b5c52aa8.dat; fi; if test -f output_performance.npz; then mv output_performance.npz /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/outputs/dataset_340d714b-ea61-4f02-9a06-3a509f31fc47.dat; fi;", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2024-06-28T09:00:51.154276", - "dependencies": [], - "exit_code": 0, - "external_id": "66123", - "galaxy_version": "24.0", - "handler": null, - "history_id": "52e55242f7275d02", - "id": "63581132e3d3fcd7", - "inputs": { - "config_json": { - "id": "8638ae59da399d18", - "src": "hda", - "uuid": "249a96e0-a3d5-42bd-8d9f-8aeb075051f2" - }, - "input_train_npy_path": { - "id": "52e55242f7275d02", - "src": "hda", - "uuid": "245bf14d-1659-4578-a68b-afb1ce9308f1" - } - }, - "job_messages": [], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output_model_pth_path": { - "id": "63581132e3d3fcd7", - "src": "hda", - "uuid": "d4a02c99-cb7c-4e22-a5bb-da3d294518d4" - }, - "output_performance_npz_path": { - "id": "97f585e74de64884", - "src": "hda", - "uuid": "340d714b-ea61-4f02-9a06-3a509f31fc47" - }, - "output_train_data_npz_path": { - "id": "3567654777edac40", - "src": "hda", - "uuid": "c853af5a-bc40-41fe-8d2f-8380b5c52aa8" - } - }, - "params": { - "__input_ext": "\"npy\"", - "chromInfo": "\"/Users/pau/projects/galaxy/tool-data/shared/ucsc/chrom/?.len\"", - "dbkey": "\"?\"", - "input_model_pth_path": null, - "outname_output_model_pth_path": "\"output_model.pth\"", - "outname_output_performance_npz_path": "\"output_performance.npz\"", - "outname_output_train_data_npz_path": "\"output_train_data.npz\"" - }, - "state": "ok", - "stderr": "", - "stdout": "2024-06-28 11:00:56,519 [MainThread ] [INFO ] Executing biobb_pytorch.mdae.train_mdae Version: 4.2.1\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Copy: ./input_train_npy_path.npy to /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Start Training:\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Device: cpu\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Train input file: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/input_train_npy_path.npy\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] File size: 119.66 KB\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of atoms: 102\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of frames for training: 80 Total number of frames: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of epochs: 50\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Partition: 0.8\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Batch size: 1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate: 0.0001\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate step size: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate gamma: 0.1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of layers: 4\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Input dimensions: 306\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Latent dimensions: 2\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Loss function: MSELoss\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Optimizer: Adam \n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Seed: 1\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Checkpoint interval: 25\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Log interval: 10\n\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Epoch 1/50, Train Loss: 0.042, Validation Loss: 0.040, LR: 0.00010, Duration: 00s, ETA: 17s\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__0.pth\n2024-06-28 11:00:59,230 [MainThread ] [INFO ] Epoch 11/50, Train Loss: 0.026, Validation Loss: 0.025, LR: 0.00010, Duration: 00s, ETA: 11s\n2024-06-28 11:01:01,832 [MainThread ] [INFO ] Epoch 21/50, Train Loss: 0.024, Validation Loss: 0.024, LR: 0.00010, Duration: 00s, ETA: 07s\n2024-06-28 11:01:03,209 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__25.pth\n2024-06-28 11:01:04,644 [MainThread ] [INFO ] Epoch 31/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 04s\n2024-06-28 11:01:07,345 [MainThread ] [INFO ] Epoch 41/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 02s\n2024-06-28 11:01:09,770 [MainThread ] [INFO ] Epoch 50/50, Train Loss: 0.022, Validation Loss: 0.022, LR: 0.00010, Duration: 00s, ETA: 00s\n2024-06-28 11:01:09,771 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__49.pth\n2024-06-28 11:01:09,775 [MainThread ] [INFO ] End Training, total time: 13s\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] Saving train data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_train_data.npz\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] File size: 1.31 KB\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] Saving evaluation data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_performance.npz\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] File size: 121.13 KB\n2024-06-28 11:01:09,825 [MainThread ] [INFO ] Saving best model to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_model.pth\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] Best model epoch: 49\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] File size: 931.57 KB\n2024-06-28 11:01:09,829 [MainThread ] [INFO ] Removed: []\n", - "tool_id": "biobb_pytorch_train_mdae", - "tool_stderr": "", - "tool_stdout": "2024-06-28 11:00:56,519 [MainThread ] [INFO ] Executing biobb_pytorch.mdae.train_mdae Version: 4.2.1\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Copy: ./input_train_npy_path.npy to /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a\n2024-06-28 11:00:56,520 [MainThread ] [INFO ] Start Training:\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Device: cpu\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] Train input file: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/input_train_npy_path.npy\n2024-06-28 11:00:56,521 [MainThread ] [INFO ] File size: 119.66 KB\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of atoms: 102\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of frames for training: 80 Total number of frames: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of epochs: 50\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Partition: 0.8\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Batch size: 1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate: 0.0001\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate step size: 100\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Learning rate gamma: 0.1\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Number of layers: 4\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Input dimensions: 306\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Latent dimensions: 2\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Loss function: MSELoss\n2024-06-28 11:00:56,522 [MainThread ] [INFO ] Optimizer: Adam \n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Seed: 1\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Checkpoint interval: 25\n2024-06-28 11:00:56,523 [MainThread ] [INFO ] Log interval: 10\n\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Epoch 1/50, Train Loss: 0.042, Validation Loss: 0.040, LR: 0.00010, Duration: 00s, ETA: 17s\n2024-06-28 11:00:56,871 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__0.pth\n2024-06-28 11:00:59,230 [MainThread ] [INFO ] Epoch 11/50, Train Loss: 0.026, Validation Loss: 0.025, LR: 0.00010, Duration: 00s, ETA: 11s\n2024-06-28 11:01:01,832 [MainThread ] [INFO ] Epoch 21/50, Train Loss: 0.024, Validation Loss: 0.024, LR: 0.00010, Duration: 00s, ETA: 07s\n2024-06-28 11:01:03,209 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__25.pth\n2024-06-28 11:01:04,644 [MainThread ] [INFO ] Epoch 31/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 04s\n2024-06-28 11:01:07,345 [MainThread ] [INFO ] Epoch 41/50, Train Loss: 0.023, Validation Loss: 0.023, LR: 0.00010, Duration: 00s, ETA: 02s\n2024-06-28 11:01:09,770 [MainThread ] [INFO ] Epoch 50/50, Train Loss: 0.022, Validation Loss: 0.022, LR: 0.00010, Duration: 00s, ETA: 00s\n2024-06-28 11:01:09,771 [MainThread ] [INFO ] Saving: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/checkpoint_epoch__49.pth\n2024-06-28 11:01:09,775 [MainThread ] [INFO ] End Training, total time: 13s\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] Saving train data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_train_data.npz\n2024-06-28 11:01:09,782 [MainThread ] [INFO ] File size: 1.31 KB\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] Saving evaluation data to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_performance.npz\n2024-06-28 11:01:09,821 [MainThread ] [INFO ] File size: 121.13 KB\n2024-06-28 11:01:09,825 [MainThread ] [INFO ] Saving best model to: /private/var/folders/yy/x7prx15n63zdp_f5jxc3z6pr0000gn/T/tmpeqf59nxd/job_working_directory/000/3/working/7916b6d5-6698-425a-8aa9-c3c4a359995a/output_model.pth\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] Best model epoch: 49\n2024-06-28 11:01:09,826 [MainThread ] [INFO ] File size: 931.57 KB\n2024-06-28 11:01:09,829 [MainThread ] [INFO ] Removed: 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