Mercurial > repos > tduigou > cloning_simulation
view output.json @ 15:074a76e84b80 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 13:39:57 +0000 |
| parents | 16ccb36aa8e3 |
| children | fbb241adf6c2 |
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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": "1e8e6749bc68d8e8", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "e2ca7f14a85a8d44", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/2/0/d/dataset_20d4061a-81e4-4915-a841-ae8aa595c7b4.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat:part_A.gb,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat:part_B.gb,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat:part_C.gb,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat:part_D.gb,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat:part_E.gb,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat:part_G.gb,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat:part_H.gb,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat:part_I.gb,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat:part_J.gb,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat:part_K.gb,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.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/tmpm1fyob3t/job_working_directory/000/14/outputs/dataset_64d1d8ac-32f0-4095-be30-22eee31e24a4.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:02:32.643157", "dependencies": [], "exit_code": 0, "external_id": "172939", "galaxy_version": "24.2", "handler": null, "history_id": "e2ca7f14a85a8d44", "id": "a36db940f4513bd9", "inputs": { "assembly_csv": { "id": "1e8e6749bc68d8e8", "src": "hda", "uuid": "20d4061a-81e4-4915-a841-ae8aa595c7b4" }, "genbank_files1": { "id": "e2ca7f14a85a8d44", "src": "hda", "uuid": "dd844d61-fc05-41d9-8179-21233649407d" }, "genbank_files10": { "id": "fbec4a551130f847", "src": "hda", "uuid": "b8fd4610-2f6d-475c-8405-8bf8c2bc0306" }, "genbank_files11": { "id": "5bd8560352cb0b69", "src": "hda", "uuid": "09f4b020-4e7b-4939-b3ba-348f91cb92bc" }, "genbank_files12": { "id": "cb2fe7fb50f38553", "src": "hda", "uuid": "eb730263-9442-4dca-a2dc-34b1cae450d7" }, "genbank_files2": { "id": "62e98d1a229b6ef5", "src": "hda", "uuid": "cb2362f3-4b32-46cc-a227-dc15742bf9e7" }, "genbank_files3": { "id": "f8fe24202fc5b2e5", "src": "hda", "uuid": "6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a" }, "genbank_files4": { "id": "0d58e12bbe78a903", "src": "hda", "uuid": "33e804b2-0fbe-4844-9b5d-420e8a2db772" }, "genbank_files5": { "id": "3937d5ff7c0e1373", "src": "hda", "uuid": "2db3825c-538b-483f-b6ff-8dc4ecc03780" }, "genbank_files6": { "id": "473b1992d5f5b84f", "src": "hda", "uuid": "048ee7ed-5f4c-41ef-aed4-f2cf975aac92" }, "genbank_files7": { "id": "9b5c1fe7a52a75e0", "src": "hda", "uuid": "c505c12e-7089-4a17-a605-4f11dad6f1d7" }, "genbank_files8": { "id": "c32c50a47ebf8564", "src": "hda", "uuid": "4912f12d-0842-46b7-8aaf-2a94a52f04f8" }, "genbank_files9": { "id": "5f035ce298b798b0", "src": "hda", "uuid": "b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "62e98d1a229b6ef5", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "182eefa577c2a56d", "src": "hda", "uuid": "991437a5-bbe4-4adb-8831-c9a871adb17f" }, "__new_primary_file_construct_gb|construct_2__": { "id": "979fd704a8b37879", "src": "hda", "uuid": "9ebdb527-8609-4bc8-85a3-f8775156c356" }, "__new_primary_file_construct_gb|construct_3__": { "id": "b53ff5232a859d40", "src": "hda", "uuid": "235361e4-93cc-4b56-ad81-c33ce8f593f0" }, "__new_primary_file_construct_gb|construct_4__": { "id": "1ce0e68b6cd95b3c", "src": "hda", "uuid": "49100d5c-134b-4cb0-a86b-2cf03a336b1c" }, "output_zip": { "id": "a36db940f4513bd9", "src": "hda", "uuid": "64d1d8ac-32f0-4095-be30-22eee31e24a4" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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, 2.58it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/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, 2.58it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/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": "2025-05-26T12:02:45.106475", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 0, "time_seconds": 53.48332858085632, "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": "035124d32eef3033", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "f8fe24202fc5b2e5", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/1/6/f/dataset_16f6d475-b614-4427-9c06-95a0d56d3c92.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.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/tmpm1fyob3t/job_working_directory/000/17/outputs/dataset_505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:02:55.721992", "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": "173310", "galaxy_version": "24.2", "handler": null, "history_id": "62e98d1a229b6ef5", "id": "b53ff5232a859d40", "inputs": { "assembly_csv": { "id": "035124d32eef3033", "src": "hda", "uuid": "16f6d475-b614-4427-9c06-95a0d56d3c92" }, "genbank_files1": { "id": "1fe688df02a38cc2", "src": "hda", "uuid": "96a8f769-3544-4407-b064-04f24a733896" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "0d58e12bbe78a903", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "f970a04054a49348", "src": "hda", "uuid": "ff8ea1a1-10ff-4416-b944-a78a4fd3e72e" }, "__new_primary_file_construct_gb|construct_2__": { "id": "ae9b306409c7f353", "src": "hda", "uuid": "7afee741-2c2b-4e3b-a947-819ebb5b67b4" }, "__new_primary_file_construct_gb|construct_3__": { "id": "791483eeafbe6bcb", "src": "hda", "uuid": "c820ba84-23dc-4e1c-b2de-abed54b17015" }, "output_zip": { "id": "cd80768c91dddfb6", "src": "hda", "uuid": "505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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, 4.35it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.33it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.53it/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, 4.35it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.33it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.53it/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": "2025-05-26T12:03:07.748084", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 1, "time_seconds": 22.338457345962524, "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": "c9169186136d0f27", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "3937d5ff7c0e1373", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/7/c/dataset_f7c9ad78-8e74-4a3c-9579-80a93ac923de.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.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/tmpm1fyob3t/job_working_directory/000/21/outputs/dataset_3fc625c8-722f-4efb-9c09-0d664dec2a9d.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:03:18.983816", "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": "173689", "galaxy_version": "24.2", "handler": null, "history_id": "f8fe24202fc5b2e5", "id": "cd80768c91dddfb6", "inputs": { "assembly_csv": { "id": "c9169186136d0f27", "src": "hda", "uuid": "f7c9ad78-8e74-4a3c-9579-80a93ac923de" }, "genbank_files1": { "id": "f14f22136515e5fc", "src": "hda", "uuid": "f56913bd-fc92-4122-8cf1-d9b1c60e8385" }, "genbank_files2": { "id": "d00c2a698869e2f3", "src": "hda", "uuid": "3b4e75b3-e6a6-459a-a959-d43ce00c3701" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "473b1992d5f5b84f", "src": "hdca" } }, "outputs": { "output_zip": { "id": "0bb6e1adb7bbb7d6", "src": "hda", "uuid": "3fc625c8-722f-4efb-9c09-0d664dec2a9d" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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, 2.40it/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, 2.40it/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": "2025-05-26T12:03:31.119796", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 2, "time_seconds": 23.440476655960083, "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": "b66a1bb5ed06a6bf", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "9b5c1fe7a52a75e0", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/b/4/dataset_fb426ceb-2615-447d-b04e-ae4253af648d.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat:GFP.gb,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat:p15A_kan.gb,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat:promoter.gb,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat:RFP.gb,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.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/tmpm1fyob3t/job_working_directory/000/28/outputs/dataset_45ef7ed5-48aa-4286-ac51-3391b593eb7c.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:03:51.986652", "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": "174270", "galaxy_version": "24.2", "handler": null, "history_id": "0d58e12bbe78a903", "id": "0bb6e1adb7bbb7d6", "inputs": { "assembly_csv": { "id": "b66a1bb5ed06a6bf", "src": "hda", "uuid": "fb426ceb-2615-447d-b04e-ae4253af648d" }, "genbank_files1": { "id": "4c26f2b3928e5c2b", "src": "hda", "uuid": "ecb057a2-dbf8-4105-b55e-d726ec1e9693" }, "genbank_files2": { "id": "7f1b25c57f1b4097", "src": "hda", "uuid": "498fe703-52c3-4162-be00-93f49f00689d" }, "genbank_files3": { "id": "cbd9b7f3981a10ff", "src": "hda", "uuid": "d402c2ac-ca2d-46b6-b9d3-989739678de1" }, "genbank_files4": { "id": "8f1ec376bf339086", "src": "hda", "uuid": "1124ff36-f61b-4932-adc6-0b6de5a888ae" }, "genbank_files5": { "id": "a91e9fd0ce2e3c53", "src": "hda", "uuid": "8fe51091-39c5-4aa6-b0ec-fbc34712e405" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "c32c50a47ebf8564", "src": "hdca" } }, "outputs": { "output_zip": { "id": "2be24ce9bdbc87e1", "src": "hda", "uuid": "45ef7ed5-48aa-4286-ac51-3391b593eb7c" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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, 48.97it/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, 48.97it/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": "2025-05-26T12:04:01.978111", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 3, "time_seconds": 30.717636823654175, "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": "5493159c7d57114c", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "5f035ce298b798b0", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/4/9/a/dataset_49af2c08-3ad4-4940-ae84-f93df3c0dd8a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat:BBa_E0040_GFP.gb,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat:BBa_J23119_prom.gb,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat:BBa_J61048_term.gb,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.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/tmpm1fyob3t/job_working_directory/000/35/outputs/dataset_3f72ea64-02f3-413e-9d9a-5c43eaaadf14.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:04:23.734013", "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": "174889", "galaxy_version": "24.2", "handler": null, "history_id": "3937d5ff7c0e1373", "id": "2be24ce9bdbc87e1", "inputs": { "assembly_csv": { "id": "5493159c7d57114c", "src": "hda", "uuid": "49af2c08-3ad4-4940-ae84-f93df3c0dd8a" }, "genbank_files1": { "id": "8d7d89366ae6734b", "src": "hda", "uuid": "894d0a5e-2d87-4861-85cb-b5cae83b19cb" }, "genbank_files2": { "id": "30133c2583e745a4", "src": "hda", "uuid": "315f1808-e9c5-45fb-8cb8-b71e8e1c8366" }, "genbank_files3": { "id": "d3fd00b679818750", "src": "hda", "uuid": "b67a6264-6208-4b44-8fd4-47ba3f96faee" }, "genbank_files4": { "id": "a5593c3e02c9d8f6", "src": "hda", "uuid": "ce3a0b5e-0344-4422-b84a-84904818396b" }, "genbank_files5": { "id": "fb42640a8a596816", "src": "hda", "uuid": "b7dcace3-2dbd-49db-94ac-98485bf522aa" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "fbec4a551130f847", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "f1bdbab1d80457ac", "src": "hda", "uuid": "8a7dec58-9e11-4bbf-a945-3910d02c89d9" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "588795470b41a739", "src": "hda", "uuid": "ee52fe89-63a0-498c-bdbb-ec9fe5b72eca" }, "__new_primary_file_construct_gb|C3_final__": { "id": "de619fffe043835f", "src": "hda", "uuid": "6b8fe4a1-1743-4ec5-a12e-6b7b267efa08" }, "output_zip": { "id": "a072914da4208f87", "src": "hda", "uuid": "3f72ea64-02f3-413e-9d9a-5c43eaaadf14" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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 [00:00<00:00, 2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.66it/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 [00:00<00:00, 2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.66it/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": "2025-05-26T12:04:36.963198", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 4, "time_seconds": 34.648075580596924, "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": "d61e70858d065388", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "5bd8560352cb0b69", "src": "hdca" }, "genbank_files": { "id": "cb2fe7fb50f38553", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/2/3/dataset_f2390ba6-b891-4c75-b5b4-881fabe15212.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat' --domesticated_seq '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat:part_A.gb,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat:part_B.gb,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat:part_C.gb,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat:part_D.gb,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat:part_E.gb,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat:part_H.gb,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat:part_I.gb,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat:part_J.gb,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat:part_K.gb,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.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/tmpm1fyob3t/job_working_directory/000/49/outputs/dataset_b5c1d918-9a86-47ac-9fd0-0d1eeecb3515.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:05:17.468278", "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": "176006", "galaxy_version": "24.2", "handler": null, "history_id": "473b1992d5f5b84f", "id": "52d2dbb7944a53fc", "inputs": { "assembly_csv": { "id": "d61e70858d065388", "src": "hda", "uuid": "f2390ba6-b891-4c75-b5b4-881fabe15212" }, "domesticated_input1": { "id": "201ce005b4eba284", "src": "hda", "uuid": "b263e11f-1d52-45d4-8679-8bb23668154a" }, "domesticated_input2": { "id": "ccacdf94e033958e", "src": "hda", "uuid": "c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee" }, "domesticated_input3": { "id": "71f633fb8d250097", "src": "hda", "uuid": "ddcb9f93-9b4f-41e3-a1df-5537b6326a78" }, "domesticated_input4": { "id": "23971c9dcf22198b", "src": "hda", "uuid": "99bac98d-1cbf-4ab1-a680-49cdb721e447" }, "domesticated_input5": { "id": "60438d790668bc40", "src": "hda", "uuid": "685cd571-80b5-4c03-b247-4fb51e199639" }, "genbank_files1": { "id": "562cdacb0f854350", "src": "hda", "uuid": "dfe71b71-2603-48cf-bf59-772724abea0f" }, "genbank_files2": { "id": "b5f666ac47f1f830", "src": "hda", "uuid": "09260017-ac9e-4868-b386-27ef07ca03a8" }, "genbank_files3": { "id": "316b2bf479d3691f", "src": "hda", "uuid": "84e57026-4e85-4a63-b66a-8bae5b767f0c" }, "genbank_files4": { "id": "52d2dbb7944a53fc", "src": "hda", "uuid": "7d26d36d-bb1c-4f83-be4f-3311e4ec2441" }, "genbank_files5": { "id": "6d0420a098f813ba", "src": "hda", "uuid": "8a0ff1e5-aaf7-461e-b642-b60e5cf13132" }, "genbank_files6": { "id": "98086fd4fda4fb74", "src": "hda", "uuid": "f94fb7c9-761b-4dc1-8caa-a02ee7892c59" }, "genbank_files7": { "id": "1e3f8509b9833e4e", "src": "hda", "uuid": "c7e408b5-927b-4966-8d1f-08de3b41fc34" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "1e8e6749bc68d8e8", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "825e5e92a55932c1", "src": "hda", "uuid": "fd97fd7a-08b9-42ba-ae2a-022c8be1b219" }, "__new_primary_file_construct_gb|construct_2__": { "id": "4a8ace5529c8c3e9", "src": "hda", "uuid": "b9201d86-ee66-45ac-99a5-09d3ca161d8b" }, "__new_primary_file_construct_gb|construct_3__": { "id": "f0d76a7bda3035c9", "src": "hda", "uuid": "7c74cbab-8a62-43a2-95f3-00919cc11fa7" }, "__new_primary_file_construct_gb|construct_4__": { "id": "640790f555d03105", "src": "hda", "uuid": "a450e128-38e8-4eb5-82a1-304b04c68510" }, "output_zip": { "id": "50943f113f3eedaf", "src": "hda", "uuid": "b5c1d918-9a86-47ac-9fd0-0d1eeecb3515" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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, 2.40it/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, 2.40it/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": "2025-05-26T12:05:29.989306", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 5, "time_seconds": 53.09692740440369, "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": "d71403ee85b47d8d", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "a36db940f4513bd9", "src": "hdca" }, "topology": "circular" }, "job": { "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/3/c/1/dataset_3c1221bc-ba53-4ede-899c-e4defbe838eb.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat:part_A.gb,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat:part_B.gb,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat:part_C.gb,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat:part_D.gb,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat:part_E.gb,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat:part_F.gb,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat:part_G.gb,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat:part_H.gb,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat:part_I.gb,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat:part_J.gb,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat:part_K.gb,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.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/tmpm1fyob3t/job_working_directory/000/63/outputs/dataset_02e7ea5e-6c8f-419d-82de-476bccc550ec.dat'", "command_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T12:06:09.749817", "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": "177047", "galaxy_version": "24.2", "handler": null, "history_id": "9b5c1fe7a52a75e0", "id": "640790f555d03105", "inputs": { "assembly_csv": { "id": "d71403ee85b47d8d", "src": "hda", "uuid": "3c1221bc-ba53-4ede-899c-e4defbe838eb" }, "domesticated_input1": { "id": "740094ed962e7335", "src": "hda", "uuid": "68ee2e69-c2d9-43cd-851e-0b660884cac2" }, "domesticated_input10": { "id": "06981e06b6149081", "src": "hda", 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"output_zip": { "id": "7d40cd3e06526c58", "src": "hda", "uuid": "02e7ea5e-6c8f-419d-82de-476bccc550ec" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "chromInfo": "\"/tmp/tmpm1fyob3t/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, 2.43it/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, 2.43it/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": "2025-05-26T12:06:22.164674", "user_email": "planemo@galaxyproject.org", "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 6, "time_seconds": 52.117783308029175, "tool_id": "cloning_simulation", 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