Mercurial > repos > tduigou > cloning_simulation
view output.json @ 8:07e902da89ad draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 09:23:51 +0000 |
| parents | 296e5145a862 |
| children | 0be569bd5443 |
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{ "summary": { "num_errors": 0, "num_failures": 0, "num_skips": 0, "num_tests": 7 }, "tests": [ { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "0a696a8b22798e06", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "cb6d3fbb91be6861", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/b/a/a/dataset_baa59b14-7fb5-4efc-a75d-228d26b70adc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/14/outputs/dataset_49164d85-9bff-47f5-b8ee-de001d155fd3.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:56:03.115650", "dependencies": [], "exit_code": 0, "external_id": "78665", "galaxy_version": "24.2", "handler": null, "history_id": "cb6d3fbb91be6861", "id": "2ff5b0f6b4cfbb73", "inputs": { "assembly_csv": { "id": "0a696a8b22798e06", "src": "hda", "uuid": "baa59b14-7fb5-4efc-a75d-228d26b70adc" }, "genbank_files1": { "id": "cb6d3fbb91be6861", "src": "hda", "uuid": "f7bde375-2c6b-4e23-9117-e96bb4c3f6e6" }, "genbank_files10": { "id": "7ede2556a40dc9ba", "src": "hda", "uuid": "3217492e-bc97-4d61-87fd-b9d1f2e4534d" }, "genbank_files11": { "id": "76608081d307dc20", "src": "hda", "uuid": "f8f04302-598c-4596-99a1-6c7d84b613d6" }, "genbank_files12": { "id": "0551bf01e3dbca02", "src": "hda", "uuid": "9f67cbfd-ca06-4926-b042-74a0d43b585a" }, "genbank_files2": { "id": "18a1e53d7b8ec0fa", "src": "hda", "uuid": "ba5c9d10-e47e-4ced-9aaf-a51bf18e7932" }, "genbank_files3": { "id": "afdf3d24f0e34eea", "src": "hda", "uuid": "bf6e6482-afaa-4790-ac74-23f532fa48ad" }, "genbank_files4": { "id": "285751a21c9d1d68", "src": "hda", "uuid": "1b8c7b47-fdba-4046-953a-89dc0c07ae14" }, "genbank_files5": { "id": "48e4779cf88cf124", "src": "hda", "uuid": "5f5321b9-fa9a-4a73-9573-890d0c00209d" }, "genbank_files6": { "id": "2bf3ecab9316a382", "src": "hda", "uuid": "8557a762-7c36-4111-a015-2b61caad4e5b" }, "genbank_files7": { "id": "d51bf47fbc922335", "src": "hda", "uuid": "f7000fc2-7e04-4561-875c-b84614f51966" }, "genbank_files8": { "id": "590bb56cc83504dc", "src": "hda", "uuid": "3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09" }, "genbank_files9": { "id": "ff96e44e65db99f8", "src": "hda", "uuid": "e3b26d77-5d05-4a0f-adf7-016bf86c5eb3" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "18a1e53d7b8ec0fa", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "be5466d8eb2c2229", "src": "hda", "uuid": "2c83aaa9-63df-43a5-b008-9a361a9fc312" }, "__new_primary_file_construct_gb|construct_2__": { "id": "a37f81f30817f4ff", "src": "hda", "uuid": "8ba2ce56-ba8b-4ff8-bcc0-54d0a2ad3b09" }, "__new_primary_file_construct_gb|construct_3__": { "id": "b4705f371a43addc", "src": "hda", "uuid": "47741e71-6bf6-46ec-9353-25bb48d895ed" }, "__new_primary_file_construct_gb|construct_4__": { "id": "0dc911fcb05967a3", "src": "hda", "uuid": "6aa740ec-6985-4d66-8427-b1652fa06f3a" }, "output_zip": { "id": "2ff5b0f6b4cfbb73", "src": "hda", "uuid": "49164d85-9bff-47f5-b8ee-de001d155fd3" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:56:15.534051", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 0, "time_seconds": 54.95904994010925, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-0" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "e01f0df21d75058c", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "afdf3d24f0e34eea", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/b/2/dataset_5b2e01d9-e63b-45e1-8523-e88570aecbd1.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/17/outputs/dataset_81c8307a-8e03-4975-b3ec-1115f4f47284.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:56:26.250368", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", "version": "0.1.11" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", "version": "1.85" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", "version": "0.1.10" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", "version": "2.2.3" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", "version": "2.0.12" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", "version": "0.3.9" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", "version": "0.1.8" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "79009", "galaxy_version": "24.2", "handler": null, "history_id": "18a1e53d7b8ec0fa", "id": "b4705f371a43addc", "inputs": { "assembly_csv": { "id": "e01f0df21d75058c", "src": "hda", "uuid": "5b2e01d9-e63b-45e1-8523-e88570aecbd1" }, "genbank_files1": { "id": "bc8da7662961ae94", "src": "hda", "uuid": "5633084d-0123-48ba-b733-086550a95944" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "285751a21c9d1d68", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "d8c348e4a6c18790", "src": "hda", "uuid": "39e12d2a-e4aa-491e-bb74-be0d48efaa36" }, "__new_primary_file_construct_gb|construct_2__": { "id": "cc98bdb1867cbf6a", "src": "hda", "uuid": "dbc568c1-dd73-4973-aa7a-f33cb279cbb7" }, "__new_primary_file_construct_gb|construct_3__": { "id": "dd60b22cea40a264", "src": "hda", "uuid": "3d0514f2-d798-484f-add3-d04103fef517" }, "output_zip": { "id": "cb5bc2d1019b090c", "src": "hda", "uuid": "81c8307a-8e03-4975-b3ec-1115f4f47284" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:56:38.283009", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 1, "time_seconds": 22.636474609375, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-1" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "c6996082322986ef", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "48e4779cf88cf124", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/3/6/c/dataset_36c9642c-c980-4a5f-babe-e1140450965b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/21/outputs/dataset_dd39a396-84ad-4350-8d9b-a0efafd5ea2a.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:56:49.662294", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", "version": "0.1.11" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", "version": "1.85" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", "version": "0.1.10" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", "version": "2.2.3" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", "version": "2.0.12" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", "version": "0.3.9" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", "version": "0.1.8" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "79436", "galaxy_version": "24.2", "handler": null, "history_id": "afdf3d24f0e34eea", "id": "cb5bc2d1019b090c", "inputs": { "assembly_csv": { "id": "c6996082322986ef", "src": "hda", "uuid": "36c9642c-c980-4a5f-babe-e1140450965b" }, "genbank_files1": { "id": "ff6721ae641686bd", "src": "hda", "uuid": "fd7feec8-d839-4aac-ba59-54d4042d72d4" }, "genbank_files2": { "id": "898f771988549b05", "src": "hda", "uuid": "097d3af5-48d7-4b15-9063-19cc11585d82" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "2bf3ecab9316a382", "src": "hdca" } }, "outputs": { "output_zip": { "id": "b995dfb8c32b92b7", "src": "hda", "uuid": "dd39a396-84ad-4350-8d9b-a0efafd5ea2a" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.23it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.23it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:57:02.321903", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 2, "time_seconds": 23.856895685195923, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-2" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "9d9573fdc2182066", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "d51bf47fbc922335", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/2/5/1/dataset_251d413f-0fe8-42cd-8a76-7ef77cde6f15.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat:GFP.gb,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat:p15A_kan.gb,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat:promoter.gb,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat:RFP.gb,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/28/outputs/dataset_8e6b31eb-84b3-4184-92eb-33384ae50857.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:57:24.342653", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", "version": "0.1.11" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", "version": "1.85" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", "version": "0.1.10" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", "version": "2.2.3" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", "version": "2.0.12" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", "version": "0.3.9" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", "version": "0.1.8" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "80040", "galaxy_version": "24.2", "handler": null, "history_id": "285751a21c9d1d68", "id": "b995dfb8c32b92b7", "inputs": { "assembly_csv": { "id": "9d9573fdc2182066", "src": "hda", "uuid": "251d413f-0fe8-42cd-8a76-7ef77cde6f15" }, "genbank_files1": { "id": "241cfac882733d83", "src": "hda", "uuid": "7d893bbf-b4e0-4d64-bafc-21ba1566237d" }, "genbank_files2": { "id": "7ada2c781708b1e8", "src": "hda", "uuid": "cc2314fa-924f-47c0-b89a-661fb78790a4" }, "genbank_files3": { "id": "4deb8a541e3f0671", "src": "hda", "uuid": "8d097c97-7bd5-48eb-9f9e-f5b92ce19458" }, "genbank_files4": { "id": "cdcc9004d7157de8", "src": "hda", "uuid": "59189305-e832-4191-be7c-496c01c8aba6" }, "genbank_files5": { "id": "33fad5084f4d4cb5", "src": "hda", "uuid": "402500d7-6532-4008-9445-c0cf7fed5350" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "590bb56cc83504dc", "src": "hdca" } }, "outputs": { "output_zip": { "id": "4f510c4214d7d568", "src": "hda", "uuid": "8e6b31eb-84b3-4184-92eb-33384ae50857" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:57:34.740635", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 3, "time_seconds": 32.283992767333984, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-3" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "017df84d4155fcba", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "ff96e44e65db99f8", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/f/d/9/dataset_fd913c0f-ea98-4b8d-a170-961146c201d5.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat:BBa_E0040_GFP.gb,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat:BBa_J23119_prom.gb,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat:BBa_J23119_prom_flawed.gb,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat:BBa_J61048_term.gb,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/35/outputs/dataset_a3f2eab1-bbe1-401e-b436-b7ffc698ee3a.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:57:56.917009", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", "version": "0.1.11" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", "version": "1.85" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", "version": "0.1.10" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", "version": "2.2.3" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", "version": "2.0.12" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", "version": "0.3.9" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", "version": "0.1.8" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "80672", "galaxy_version": "24.2", "handler": null, "history_id": "48e4779cf88cf124", "id": "4f510c4214d7d568", "inputs": { "assembly_csv": { "id": "017df84d4155fcba", "src": "hda", "uuid": "fd913c0f-ea98-4b8d-a170-961146c201d5" }, "genbank_files1": { "id": "1745fab1994e918a", "src": "hda", "uuid": "38402f39-a1d3-495e-afed-bf8335b4cdb6" }, "genbank_files2": { "id": "9f4b12edd1240647", "src": "hda", "uuid": "9c8ea453-16b9-4b9d-b171-9d5c0322adf9" }, "genbank_files3": { "id": "070cf47a9114ebf0", "src": "hda", "uuid": "31a46fbb-0267-42e3-b9d3-c60804edd30c" }, "genbank_files4": { "id": "176efb58f023067c", "src": "hda", "uuid": "e278e6ea-3146-49fa-a4f5-becf766e4f5e" }, "genbank_files5": { "id": "2c38922866e3bd19", "src": "hda", "uuid": "6a19d37f-54e1-4c94-a2b1-1a7f37820aad" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "7ede2556a40dc9ba", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "e9bea5372f4a6a20", "src": "hda", "uuid": "80f480c8-264d-428b-8b95-253cd89d7764" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "1290d6537f2937e3", "src": "hda", "uuid": "7b7b6524-575a-4dfc-800c-dc0d3e8ece79" }, "__new_primary_file_construct_gb|C3_final__": { "id": "cd293a8cb9d8e7b5", "src": "hda", "uuid": "7be9e218-0841-46cd-ac62-5686969f6935" }, "output_zip": { "id": "3651b2c7591f0e47", "src": "hda", "uuid": "a3f2eab1-bbe1-401e-b436-b7ffc698ee3a" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:58:09.572798", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 4, "time_seconds": 34.93839716911316, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-4" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "b1a8f56fe428091e", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "76608081d307dc20", "src": "hdca" }, "genbank_files": { "id": "0551bf01e3dbca02", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/9/7/b/dataset_97b16fa9-53ab-4e65-9de7-e30112bcdd06.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat' --domesticated_seq '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/49/outputs/dataset_2bca238e-5421-456d-bf98-1bd44e65fc76.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:58:50.541909", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", "version": "0.1.11" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", "version": "1.85" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", "version": "0.1.10" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", "version": "2.2.3" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", "version": "2.0.12" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", "version": "0.3.9" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", "version": "0.1.8" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "81731", "galaxy_version": "24.2", "handler": null, "history_id": "2bf3ecab9316a382", "id": "aa893e5f7beb4eb8", "inputs": { "assembly_csv": { "id": "b1a8f56fe428091e", "src": "hda", "uuid": "97b16fa9-53ab-4e65-9de7-e30112bcdd06" }, "domesticated_input1": { "id": "dbc527c8f70438a2", "src": "hda", "uuid": "ef3f0423-f1dd-462b-8d68-e68cd6d59d82" }, "domesticated_input2": { "id": "a3ea165695c1e088", "src": "hda", "uuid": "ea297609-87c4-4bfc-abfd-084fbcc94d5b" }, "domesticated_input3": { "id": "d4fcfbec208c480f", "src": "hda", "uuid": "60d919ff-9b54-4856-b3d0-9836114c2575" }, "domesticated_input4": { "id": "b53993d77cff267e", "src": "hda", "uuid": "08efef6d-13c4-4e1b-a155-859e0a0df989" }, "domesticated_input5": { "id": "e1a323c2b9a73ada", "src": "hda", "uuid": "e72facc2-0bd8-49e8-94e6-6b255853b030" }, "genbank_files1": { "id": "03a53f60ebb3b30b", "src": "hda", "uuid": "823cfc4c-98db-494d-a03b-5181179a3581" }, "genbank_files2": { "id": "949b6e5fb08e3b2e", "src": "hda", "uuid": "60a53b2c-927e-4c33-b6b0-2e927266044e" }, "genbank_files3": { "id": "4b14363353165bd2", "src": "hda", "uuid": "d357996d-45c3-4715-b8eb-ea6bb836b18e" }, "genbank_files4": { "id": "aa893e5f7beb4eb8", "src": "hda", "uuid": "dacfd7e2-f5ff-4821-8d70-f73307f7997e" }, "genbank_files5": { "id": "e33440187009b2c6", "src": "hda", "uuid": "9b3f9357-c1cc-43c9-a81c-c100483b3a0d" }, "genbank_files6": { "id": "ef97dc51810891e7", "src": "hda", "uuid": "5e43150c-3c7c-4072-9720-fdc085cd6d8b" }, "genbank_files7": { "id": "16b078cfbe5cb4fb", "src": "hda", "uuid": "2de75a41-7673-4cef-aa63-2cf6d9466e8c" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "0a696a8b22798e06", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "08065af9f1d51b0a", "src": "hda", "uuid": "4837c85e-ba71-482d-91d1-be3e3179ee5a" }, "__new_primary_file_construct_gb|construct_2__": { "id": "23c03036acf6de8c", "src": "hda", "uuid": "a898af9c-3721-4b84-8ebc-790dc376316c" }, "__new_primary_file_construct_gb|construct_3__": { "id": "950510fee01c22f4", "src": "hda", "uuid": "be8dfa79-0421-418a-9822-af3e69e3bd0a" }, "__new_primary_file_construct_gb|construct_4__": { "id": "abd47de82fbecc4e", "src": "hda", "uuid": "1455799d-9a0a-46e7-8ddb-df60f983fb53" }, "output_zip": { "id": "b52f373b44c22024", "src": "hda", "uuid": "2bca238e-5421-456d-bf98-1bd44e65fc76" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:59:03.629936", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 5, "time_seconds": 53.84836268424988, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-5" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "4b6130eb686f10a7", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "2ff5b0f6b4cfbb73", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/0/4/dataset_5042213c-8bb6-48e0-9501-070e55a9a8c0.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/63/outputs/dataset_4e39f3b7-2899-410e-a32f-47270970ae14.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T08:59:44.629082", "dependencies": [ { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", "version": "0.1.11" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", "version": "1.85" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", "version": "0.1.10" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", "version": "2.2.3" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", "version": "2.0.12" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", "version": "0.3.9" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", "version": "0.1.8" }, { "cacheable": false, "dependency_resolver": { "auto_init": true, "auto_install": true, "can_uninstall_dependencies": true, "ensure_channels": "conda-forge,bioconda", "model_class": "CondaDependencyResolver", "prefix": "/home/rkhaled/miniconda3", "read_only": false, "resolver_type": "conda", "resolves_simple_dependencies": true, "use_local": false, "versionless": false }, "dependency_type": "conda", "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", "version": "3.1.5" } ], "exit_code": 0, "external_id": "82808", "galaxy_version": "24.2", "handler": null, "history_id": "d51bf47fbc922335", "id": "abd47de82fbecc4e", "inputs": { "assembly_csv": { "id": "4b6130eb686f10a7", "src": "hda", "uuid": "5042213c-8bb6-48e0-9501-070e55a9a8c0" }, "domesticated_input1": { "id": "7c76f7472621b5d0", "src": "hda", "uuid": "dd8d9744-d7f0-46ae-b26f-de961e3f5033" }, "domesticated_input10": { "id": "9bd6c123148263b6", "src": "hda", 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"output_zip": { "id": "40a6167ab839cf08", "src": "hda", "uuid": "4e39f3b7-2899-410e-a32f-47270970ae14" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", "genbank_files": null, "topology": "\"circular\"" }, "state": "ok", "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "update_time": "2025-05-26T08:59:57.832603", "user_email": "planemo@galaxyproject.org", "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 6, "time_seconds": 53.99832892417908, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-6" } ], "version": "0.1" }