Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 4:254d284a5be9 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 19 May 2025 14:09:48 +0000 |
| parents | 044d36066cb3 |
| children | e1e985913204 |
line wrap: on
line diff
--- a/output.json Fri May 16 12:40:59 2025 +0000 +++ b/output.json Mon May 19 14:09:48 2025 +0000 @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "c02153e44a10e06a", + "id": "40769e0726e5d2f9", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "a7025157dd5d3039", + "id": "fd8809ceca5b90d8", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/a/5/2/dataset_a522972a-c994-4ec0-a130-e3e1e101d126.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat:part_A.gb,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat:part_B.gb,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat:part_C.gb,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat:part_D.gb,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat:part_E.gb,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat:part_F.gb,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat:part_G.gb,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat:part_H.gb,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat:part_I.gb,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat:part_J.gb,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat:part_K.gb,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.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/tmph0r87skq/job_working_directory/000/14/outputs/dataset_109d2ac1-716e-4c47-a2b9-25e9d68cd9b7.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/4/6/dataset_14645e90-9105-48af-a071-6ea052fd4aad.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat:part_A.gb,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat:part_B.gb,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat:part_C.gb,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat:part_E.gb,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat:part_F.gb,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat:part_G.gb,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat:part_H.gb,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat:part_I.gb,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat:part_J.gb,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat:part_K.gb,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.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/tmpay0tme4v/job_working_directory/000/14/outputs/dataset_f30d906d-2ea4-4cde-b451-b7c6daf25a29.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T12:35:55.635805", + "create_time": "2025-05-19T13:45:01.696419", "dependencies": [], "exit_code": 0, - "external_id": "205109", + "external_id": "245391", "galaxy_version": "24.2", "handler": null, - "history_id": "a7025157dd5d3039", - "id": "d49d8be9932a8ee0", + "history_id": "fd8809ceca5b90d8", + "id": "d25964a649f0fc81", "inputs": { "assembly_csv": { - "id": "c02153e44a10e06a", + "id": "40769e0726e5d2f9", "src": "hda", - "uuid": "a522972a-c994-4ec0-a130-e3e1e101d126" + "uuid": "14645e90-9105-48af-a071-6ea052fd4aad" }, "genbank_files1": { - "id": "a7025157dd5d3039", + "id": "fd8809ceca5b90d8", "src": "hda", - "uuid": "eb40ee5e-5155-4303-9230-94926c63daaf" + "uuid": "4b32c6a8-b39d-4f5f-9155-307e142d9193" }, "genbank_files10": { - "id": "26800a0030991202", + "id": "171b3bd3b2ffa75e", "src": "hda", - "uuid": "184d9904-3705-424e-b3f7-e5b7b773880f" + "uuid": "e126fe05-d77c-4b33-9782-e5b1e7e6c7ad" }, "genbank_files11": { - "id": "9e9c740782c078df", + "id": "ec7f951857c74506", "src": "hda", - "uuid": "4a10d392-6ebc-413c-bd71-db425aa1aa0a" + "uuid": "234f9855-813e-4297-bbd4-d1327fb0cbad" }, "genbank_files12": { - "id": "d70a40a14f24deac", + "id": "8c74660869d2dd19", "src": "hda", - "uuid": "835878c6-84f1-465c-b34e-d177885e567d" + "uuid": "6b23e127-e4a2-41b6-98f3-4f8f7214b209" }, "genbank_files2": { - "id": "ce87194f2a532da8", + "id": "132b871e5e3014ee", "src": "hda", - "uuid": "4a9a1335-c528-438d-b80a-62b9608dbade" + "uuid": "8ef181dd-5c3a-40eb-9926-3738e1ae4be1" }, "genbank_files3": { - "id": "e52e8d0a017d5bd2", + "id": "65f48584dd2a1828", "src": "hda", - "uuid": "7caa4f6a-a734-461f-ac38-c95442632c5a" + "uuid": "babba200-2afd-434f-8797-9b10cc736ba7" }, "genbank_files4": { - "id": "4dd0eedec5562f6e", + "id": "543bb64c618cca80", "src": "hda", - "uuid": "93127db8-2409-4544-93e5-6243a6d253ef" + "uuid": "b7c5a88c-05ae-4efd-9887-47a899749178" }, "genbank_files5": { - "id": "d1cbd0905c1fc860", + "id": "e550d863bf084702", "src": "hda", - "uuid": "e292919e-0a9a-403a-aa6b-30aa552881bd" + "uuid": "7fea4ecf-be56-423d-8a11-d6491077e233" }, "genbank_files6": { - "id": "0494b81690cb2f5c", + "id": "6a73e15df176b356", "src": "hda", - "uuid": "4a7c1e6b-f470-414e-b533-7390f74a64fc" + "uuid": "e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe" }, "genbank_files7": { - "id": "edce0bc0654ca8cc", + "id": "7faba24a30f85c9d", "src": "hda", - "uuid": "7f3df904-0bc5-456a-8679-cc58d06e214e" + "uuid": "f0fe046c-6132-4bb9-b5dc-521edead32f2" }, "genbank_files8": { - "id": "052d0d471d180256", + "id": "f121a1ae40e58e96", "src": "hda", - "uuid": "a605738c-9b6d-44c6-891e-01cb729ea4dc" + "uuid": "eec197e7-d8fa-4c45-b5cb-89e51ee1db0e" }, "genbank_files9": { - "id": "5827a0347340e98b", + "id": "fc2d53421d7989de", "src": "hda", - "uuid": "10c35405-af25-41d3-9dbd-a411b4b65b98" + "uuid": "32124f40-ed9b-4d25-b74f-a4ff44581962" } }, "job_messages": [], @@ -108,60 +108,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "ce87194f2a532da8", + "id": "132b871e5e3014ee", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "68bcb17f47b988de", + "id": "6d4f2c14c91fd6e1", "src": "hda", - "uuid": "2c9a5458-38f0-4591-bb2d-452aac86ce0b" + "uuid": "32687278-a139-4ee2-bfc0-86735e813b3e" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "7cb8b41737d3d7aa", + "id": "ce0686b9d731295a", "src": "hda", - "uuid": "026f0937-350b-4ae7-96da-1e685237a8c8" + "uuid": "a78e87bc-7aa1-4e9e-8625-78450d68b18d" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "e558db6e0f20f34c", + "id": "9fb491af1d40ed73", "src": "hda", - "uuid": "df750e5d-b2f4-43f1-bf95-aa0d980bb98a" + "uuid": "6ce970af-f5f4-4193-9d0a-d1fc701d17d5" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "87544afc708050c8", + "id": "0a54ce1a82948d59", "src": "hda", - "uuid": "0ba9a694-1b4e-4ff4-b6f2-87503d04cd66" + "uuid": "b76d3345-d556-4f55-9285-6a7ce76d9150" }, "output_zip": { - "id": "d49d8be9932a8ee0", + "id": "d25964a649f0fc81", "src": "hda", - "uuid": "109d2ac1-716e-4c47-a2b9-25e9d68cd9b7" + "uuid": "f30d906d-2ea4-4cde-b451-b7c6daf25a29" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpay0tme4v/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, 2.25it/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", + "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, 2.14it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/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, 2.25it/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_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, 2.14it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/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": "2025-05-16T12:36:09.065234", + "update_time": "2025-05-19T13:45:15.319665", "user_email": "planemo@galaxyproject.org", - "user_id": "a7025157dd5d3039" + "user_id": "fd8809ceca5b90d8" }, "status": "success", "test_index": 0, - "time_seconds": 54.82133865356445, + "time_seconds": 54.20177435874939, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -173,21 +173,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "13b114ac662002c6", + "id": "e820aa9b959ea863", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "e52e8d0a017d5bd2", + "id": "65f48584dd2a1828", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/5/7/9/dataset_579b13e6-f14d-401c-88ee-b25ed3bf42dc.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.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/tmph0r87skq/job_working_directory/000/17/outputs/dataset_36e0457f-1da8-456a-86c9-20ea242688bc.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/d/1/dataset_3d1a91ee-d9ba-41fc-bd79-f012ae654250.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.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/tmpay0tme4v/job_working_directory/000/17/outputs/dataset_3327e282-d219-43e3-94d7-88fd08aa6867.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T12:36:19.661290", + "create_time": "2025-05-19T13:45:26.929597", "dependencies": [ { "cacheable": false, @@ -367,21 +367,21 @@ } ], "exit_code": 0, - "external_id": "205459", + "external_id": "245766", "galaxy_version": "24.2", "handler": null, - "history_id": "ce87194f2a532da8", - "id": "e558db6e0f20f34c", + "history_id": "132b871e5e3014ee", + "id": "9fb491af1d40ed73", "inputs": { "assembly_csv": { - "id": "13b114ac662002c6", + "id": "e820aa9b959ea863", "src": "hda", - "uuid": "579b13e6-f14d-401c-88ee-b25ed3bf42dc" + "uuid": "3d1a91ee-d9ba-41fc-bd79-f012ae654250" }, "genbank_files1": { - "id": "16385471cc722641", + "id": "82720a2239e02ea4", "src": "hda", - "uuid": "f2e8406c-fdb7-4b30-aa74-202b93292a26" + "uuid": "069f9137-705b-4e17-b931-1ebd547a7fe4" } }, "job_messages": [], @@ -392,55 +392,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "4dd0eedec5562f6e", + "id": "543bb64c618cca80", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "eb4747fb10762624", + "id": "4aace7d444c68122", "src": "hda", - "uuid": "8b9f07c0-2a2f-49db-b0b9-e3b27b5d2102" + "uuid": "24381c81-ce88-4584-94dd-e84c078419f8" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "fa2c1cd7e40ca607", + "id": "894db8882e848d71", "src": "hda", - "uuid": "694f0f93-1c26-4a8b-91ed-bcb7fe4b3784" + "uuid": "9f704297-19e6-4faf-a500-b6b64578b376" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "2c9180ba70391455", + "id": "4d49f848d91861cd", "src": "hda", - "uuid": "e57dc6e8-10e6-4527-a375-9ed583735c59" + "uuid": "ac0d0bab-faee-48eb-bdcf-f71f1ae7dff9" }, "output_zip": { - "id": "cf8958f7b0d14fa5", + "id": "314f9466454a965d", "src": "hda", - "uuid": "36e0457f-1da8-456a-86c9-20ea242688bc" + "uuid": "3327e282-d219-43e3-94d7-88fd08aa6867" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpay0tme4v/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, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/s, now=None]\r \r", + "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, 4.20it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.12it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.34it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.62it/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, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/s, now=None]\r \r", + "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, 4.20it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.12it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.34it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.62it/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": "2025-05-16T12:36:31.612352", + "update_time": "2025-05-19T13:45:38.810356", "user_email": "planemo@galaxyproject.org", - "user_id": "a7025157dd5d3039" + "user_id": "fd8809ceca5b90d8" }, "status": "success", "test_index": 1, - "time_seconds": 22.601666688919067, + "time_seconds": 23.490375518798828, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -452,21 +452,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "84906eb14284db27", + "id": "675dca381201b1fe", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "d1cbd0905c1fc860", + "id": "e550d863bf084702", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/2/0/e/dataset_20eb88b1-0fc5-476b-a409-da7f598780b6.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.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/tmph0r87skq/job_working_directory/000/21/outputs/dataset_0ffdda24-b80f-4db5-8c10-1467d34eb3a8.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/d/9/dataset_1d9ed268-bc25-40c0-a67f-439accae7e40.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.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/tmpay0tme4v/job_working_directory/000/21/outputs/dataset_b1af7192-a26f-4e6a-ba22-9aeffac2ea46.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T12:36:42.888728", + "create_time": "2025-05-19T13:45:50.704320", "dependencies": [ { "cacheable": false, @@ -646,26 +646,26 @@ } ], "exit_code": 0, - "external_id": "205894", + "external_id": "246155", "galaxy_version": "24.2", "handler": null, - "history_id": "e52e8d0a017d5bd2", - "id": "cf8958f7b0d14fa5", + "history_id": "65f48584dd2a1828", + "id": "314f9466454a965d", "inputs": { "assembly_csv": { - "id": "84906eb14284db27", + "id": "675dca381201b1fe", "src": "hda", - "uuid": "20eb88b1-0fc5-476b-a409-da7f598780b6" + "uuid": "1d9ed268-bc25-40c0-a67f-439accae7e40" }, "genbank_files1": { - "id": "1fdafe0e70c0e721", + "id": "1b1aadbedc3f334a", "src": "hda", - "uuid": "15741680-9963-4b3d-979e-792be37256f2" + "uuid": "e0f8296e-094d-4971-976b-6e534148d1d5" }, "genbank_files2": { - "id": "044728be18fd1186", + "id": "05b5deb4bb488223", "src": "hda", - "uuid": "d3de76b3-3793-46fa-990e-970e1bcb2a72" + "uuid": "608722d5-ead5-49fb-8736-04fa7ab027f3" } }, "job_messages": [], @@ -676,40 +676,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "0494b81690cb2f5c", + "id": "6a73e15df176b356", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "920c0db56b0a806b", + "id": "499c1d005d68ae46", "src": "hda", - "uuid": "0ffdda24-b80f-4db5-8c10-1467d34eb3a8" + "uuid": "b1af7192-a26f-4e6a-ba22-9aeffac2ea46" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpay0tme4v/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, 2.42it/s, now=None]\r \r", + "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, 2.05it/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, 2.42it/s, now=None]\r \r", + "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, 2.05it/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": "2025-05-16T12:36:54.097489", + "update_time": "2025-05-19T13:46:02.749327", "user_email": "planemo@galaxyproject.org", - "user_id": "a7025157dd5d3039" + "user_id": "fd8809ceca5b90d8" }, "status": "success", "test_index": 2, - "time_seconds": 22.133039951324463, + "time_seconds": 23.55416440963745, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -721,21 +721,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "df13d5ca39cba7c4", + "id": "c06583b31ad25e9f", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { - "id": "edce0bc0654ca8cc", + "id": "7faba24a30f85c9d", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/e/9/7/dataset_e971a6cf-b13e-4a65-a78d-aa22a0ea1fff.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat:GFP.gb,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat:p15A_kan.gb,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat:promoter.gb,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat:RFP.gb,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.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/tmph0r87skq/job_working_directory/000/28/outputs/dataset_5e0faa51-141c-49d1-ba84-ca8aba27508c.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/4/4/dataset_344ef380-e9d3-4729-bc6e-45a003000613.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat:GFP.gb,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat:p15A_kan.gb,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat:promoter.gb,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat:RFP.gb,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.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/tmpay0tme4v/job_working_directory/000/28/outputs/dataset_cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T12:37:15.245845", + "create_time": "2025-05-19T13:46:24.141767", "dependencies": [ { "cacheable": false, @@ -915,41 +915,41 @@ } ], "exit_code": 0, - "external_id": "206517", + "external_id": "246833", "galaxy_version": "24.2", "handler": null, - "history_id": "4dd0eedec5562f6e", - "id": "920c0db56b0a806b", + "history_id": "543bb64c618cca80", + "id": "499c1d005d68ae46", "inputs": { "assembly_csv": { - "id": "df13d5ca39cba7c4", + "id": "c06583b31ad25e9f", "src": "hda", - "uuid": "e971a6cf-b13e-4a65-a78d-aa22a0ea1fff" + "uuid": "344ef380-e9d3-4729-bc6e-45a003000613" }, "genbank_files1": { - "id": "caecbbc14917ac69", + "id": "dcd17297edd6443c", "src": "hda", - "uuid": "4f0d4258-2f50-4a4e-9271-58e8c272856e" + "uuid": "509fa87d-4af9-46f7-b323-48f8128675c8" }, "genbank_files2": { - "id": "10cd084c8017547c", + "id": "5255abeff5637f7e", "src": "hda", - "uuid": "27f67c7a-5e38-4103-a00b-a9d8234b6686" + "uuid": "02b8b6f2-43ab-4885-a9de-336d903edc55" }, "genbank_files3": { - "id": "aa3451be0c94f76e", + "id": "a30c1b2be38d49df", "src": "hda", - "uuid": "4e880afa-3f37-43a4-982e-36d750aab3d3" + "uuid": "95aa5a16-9b61-45be-94e6-35284531fcd7" }, "genbank_files4": { - "id": "a5f159065ae97d01", + "id": "70728511d187b46b", "src": "hda", - "uuid": "3746bcc6-ee0c-4936-832f-ce29f808430d" + "uuid": "17c94fe6-e0ce-4c72-9adc-5f8132a6df81" }, "genbank_files5": { - "id": "a001a939426dadd1", + "id": "db356309fe5e8361", "src": "hda", - "uuid": "788ebd7b-6247-4f96-a3d3-3c3306c210a0" + "uuid": "db6bb8ba-4682-476e-a688-be9e5cfb0afd" } }, "job_messages": [], @@ -960,40 +960,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "052d0d471d180256", + "id": "f121a1ae40e58e96", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "081ab14c99ce168b", + "id": "15b1f0554a03958d", "src": "hda", - "uuid": "5e0faa51-141c-49d1-ba84-ca8aba27508c" + "uuid": "cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpay0tme4v/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: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.70it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 44.90it/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: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.70it/s, now=None]\r \r", + "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: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 44.90it/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": "2025-05-16T12:37:25.925491", + "update_time": "2025-05-19T13:46:34.776797", "user_email": "planemo@galaxyproject.org", - "user_id": "a7025157dd5d3039" + "user_id": "fd8809ceca5b90d8" }, "status": "success", "test_index": 3, - "time_seconds": 31.832648515701294, + "time_seconds": 32.1408953666687, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1005,21 +1005,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "6af8c0d3c72d39ba", + "id": "e7b347ef21d63fab", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "5827a0347340e98b", + "id": "fc2d53421d7989de", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/4/e/d/dataset_4ed60503-3b9f-4204-a8e9-0b96f76b1e49.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat:BBa_E0040_GFP.gb,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat:BBa_J23119_prom.gb,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat:BBa_J23119_prom_flawed.gb,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat:BBa_J61048_term.gb,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.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/tmph0r87skq/job_working_directory/000/35/outputs/dataset_5776ccd7-5dca-4f21-b288-9c15a0b9cdca.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/9/7/6/dataset_976f7d99-07e5-4d5c-ab79-a96ae42760d4.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat:BBa_E0040_GFP.gb,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat:BBa_J23119_prom.gb,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat:BBa_J61048_term.gb,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.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/tmpay0tme4v/job_working_directory/000/35/outputs/dataset_deeb975f-4ae8-44d3-9c3c-51dc05e74f05.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T12:37:47.708969", + "create_time": "2025-05-19T13:46:57.146002", "dependencies": [ { "cacheable": false, @@ -1199,41 +1199,41 @@ } ], "exit_code": 0, - "external_id": "207114", + "external_id": "247581", "galaxy_version": "24.2", "handler": null, - "history_id": "d1cbd0905c1fc860", - "id": "081ab14c99ce168b", + "history_id": "e550d863bf084702", + "id": "15b1f0554a03958d", "inputs": { "assembly_csv": { - "id": "6af8c0d3c72d39ba", + "id": "e7b347ef21d63fab", "src": "hda", - "uuid": "4ed60503-3b9f-4204-a8e9-0b96f76b1e49" + "uuid": "976f7d99-07e5-4d5c-ab79-a96ae42760d4" }, "genbank_files1": { - "id": "06bb6ed11a5684d2", + "id": "0d1c6bc715df133f", "src": "hda", - "uuid": "773be428-2d30-4b95-9894-d3758634a3d0" + "uuid": "6e0453c4-6edd-4d76-9504-4cc4941610f6" }, "genbank_files2": { - "id": "f34ce69b933b349e", + "id": "7d9d065fa6859d88", "src": "hda", - "uuid": "bac673f5-074c-4810-9949-59d3b228d83c" + "uuid": "6d3c24e5-73cd-4bed-95aa-d1c361c74180" }, "genbank_files3": { - "id": "c295924a5ace6ae8", + "id": "28aa4b1f3fb7d62b", "src": "hda", - "uuid": "e5b8dfd0-6e81-47e4-b899-08976d0a1724" + "uuid": "7793541b-18cc-4f7d-a9df-12396807c368" }, "genbank_files4": { - "id": "f3a950b5ccc2e145", + "id": "7423dfb808ef4761", "src": "hda", - "uuid": "158cbebb-69fc-4333-b783-e9171b5324d6" + "uuid": "ae1611ed-a5e2-46e8-b975-613ada1bb8db" }, "genbank_files5": { - "id": "486d488c3f12b41a", + "id": "175236d72b015bf8", "src": "hda", - "uuid": "a5b6ae8b-1068-416f-b0ac-1c44e299cb87" + "uuid": "9adfafe3-b0ad-449b-8555-286ca83e65a4" } }, "job_messages": [], @@ -1244,55 +1244,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "26800a0030991202", + "id": "171b3bd3b2ffa75e", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { - "id": "62952fe061c1d5d6", + "id": "2607809b86839f90", "src": "hda", - "uuid": "fb185bc3-4c8e-4095-864e-edc42d8c87ab" + "uuid": "4e873fda-e181-4d71-b03b-61441dad6432" }, "__new_primary_file_construct_gb|C2_gfp_term__": { - "id": "14c055702e438446", + "id": "d61271ad2bd59452", "src": "hda", - "uuid": "cb6310a2-1237-4f80-9efa-f149cb896f4d" + "uuid": "1c217e77-9cfa-48b2-aabb-ccdcd23275ca" }, "__new_primary_file_construct_gb|C3_final__": { - "id": "e9ef3e2f0e439cf2", + "id": "cdfae6a044106877", "src": "hda", - "uuid": "13db93e9-4505-4542-845c-57029b5e9a89" + "uuid": "54b8bb86-f05d-4ec1-b551-7ed8ca22aedd" }, "output_zip": { - "id": "7f1cb49d27c5ee0d", + "id": "451b6ce8fd13ed5c", "src": "hda", - "uuid": "5776ccd7-5dca-4f21-b288-9c15a0b9cdca" + "uuid": "deeb975f-4ae8-44d3-9c3c-51dc05e74f05" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpay0tme4v/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, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/s, now=None]\r \r", + "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, 1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00, 1.43it/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, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/s, now=None]\r \r", + "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, 1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00, 1.43it/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": "2025-05-16T12:38:00.688550", + "update_time": "2025-05-19T13:47:10.784667", "user_email": "planemo@galaxyproject.org", - "user_id": "a7025157dd5d3039" + "user_id": "fd8809ceca5b90d8" }, "status": "success", "test_index": 4, - "time_seconds": 34.85270929336548, + "time_seconds": 35.92383527755737, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1304,25 +1304,25 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "4e0765e9771b7fbe", + "id": "8970dbe72f491b25", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "9e9c740782c078df", + "id": "ec7f951857c74506", "src": "hdca" }, "genbank_files": { - "id": "d70a40a14f24deac", + "id": "8c74660869d2dd19", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat' --domesticated_seq '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.dat' --assembly_csv '/tmp/tmph0r87skq/files/c/6/5/dataset_c652bef1-f073-431c-9e5b-956a58e85d22.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat:part_A.gb,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat:part_B.gb,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat:part_C.gb,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat:part_D.gb,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat:part_E.gb,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat:part_F.gb,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat:part_H.gb,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat:part_I.gb,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat:part_J.gb,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat:part_K.gb,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.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/tmph0r87skq/job_working_directory/000/49/outputs/dataset_a88370aa-4d36-4867-b0d6-613cc59ed01a.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat' --domesticated_seq '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.dat' --assembly_csv '/tmp/tmpay0tme4v/files/9/c/8/dataset_9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat:part_A.gb,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat:part_B.gb,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat:part_C.gb,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat:part_E.gb,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat:part_F.gb,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat:part_H.gb,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat:part_I.gb,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat:part_J.gb,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat:part_K.gb,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.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/tmpay0tme4v/job_working_directory/000/49/outputs/dataset_800320dc-d181-40bf-b1cb-541f43a838c3.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T12:38:41.107674", + "create_time": "2025-05-19T13:47:53.361341", "dependencies": [ { "cacheable": false, @@ -1502,76 +1502,76 @@ } ], "exit_code": 0, - "external_id": "208235", + "external_id": "248775", "galaxy_version": "24.2", "handler": null, - "history_id": "0494b81690cb2f5c", - "id": "1ad8534b5033158f", + "history_id": "6a73e15df176b356", + "id": "95f3db52d6362602", "inputs": { "assembly_csv": { - "id": "4e0765e9771b7fbe", + "id": "8970dbe72f491b25", "src": "hda", - "uuid": "c652bef1-f073-431c-9e5b-956a58e85d22" + "uuid": "9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc" }, "domesticated_input1": { - "id": "067523cf02b98b71", + "id": "e666d72d584b2f08", "src": "hda", - "uuid": "afe4126c-9cc0-45ec-a7d4-37816cb2132d" + "uuid": "f6d602b9-7772-4a93-969d-f0dcdad98c6a" }, "domesticated_input2": { - "id": "2f0a34076d4435df", + "id": "55c4a2e28d82e47c", "src": "hda", - "uuid": "fa8a7e9a-fa40-4e9f-a508-261fd8441292" + "uuid": "d4dc3ecb-77ff-4b28-a55a-7b263416c6c7" }, "domesticated_input3": { - "id": "a12a625822f3f961", + "id": "b7e1b2e4287fecf1", "src": "hda", - "uuid": "7ddb44a7-da6d-4215-8d11-1ba01c4f6516" + "uuid": "7d489dbd-161e-4f04-a3df-ef5b989ad1e0" }, "domesticated_input4": { - "id": "0b82bdc4f78225f4", + "id": "fc5d10a4986179ce", "src": "hda", - "uuid": "bff58a1b-e69e-4cb4-b344-79ba8800ac03" + "uuid": "4ca3c222-672a-4806-b60c-081f1b7b64cb" }, "domesticated_input5": { - "id": "5c9f1017a9cfea44", + "id": "34217302c7a82039", "src": "hda", - "uuid": "af806691-7022-4bf2-a42b-7437042cee37" + "uuid": "906707db-b3cf-40f9-af0b-1ffc143f91e8" }, "genbank_files1": { - "id": "db55fd2326eb05de", + "id": "bb3a8c61045de2bc", "src": "hda", - "uuid": "bcd311aa-69db-4f2a-9d04-90f34cd78a6f" + "uuid": "193cbd10-4b76-46d9-b377-a7f06471d4d4" }, "genbank_files2": { - "id": "551b1ccaf842a34c", + "id": "ca37518126b9f794", "src": "hda", - "uuid": "049931ba-600a-46d6-a73e-af6bd3f545e3" + "uuid": "fa31c5f5-e678-471e-b1a3-4f8a168bbee1" }, "genbank_files3": { - "id": "aa4b51af1d3e5956", + "id": "f5318c255dfd98f3", "src": "hda", - "uuid": "860e934f-31f6-4ac6-9eac-fd3abf031b08" + "uuid": "697c83fe-168b-4319-a6e5-3db90c504c8b" }, "genbank_files4": { - "id": "1ad8534b5033158f", + "id": "95f3db52d6362602", "src": "hda", - "uuid": "aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21" + "uuid": "06d4dd94-5f33-4ce0-ab0a-e6efe96ca222" }, "genbank_files5": { - "id": "67e60392c24a116d", + "id": "22334014eeb47b8b", "src": "hda", - "uuid": "3d97e337-7388-4fab-a6c3-7cb99f371f84" + "uuid": "701b72c6-ec2e-4435-b0d5-8f419811a4dd" }, "genbank_files6": { - "id": "f0035bfbf96f19ca", + "id": "aebcfa6b078c848c", "src": "hda", - "uuid": "b45031f8-71da-4365-9560-b827aa1d6794" + "uuid": "5a07f059-f6f9-49de-b0fc-3cded157f44b" }, "genbank_files7": { - "id": "d2976cafec9acf3d", + "id": "63b7227f824d465f", "src": "hda", - "uuid": "9e21455c-b124-4c01-8524-949ff16b570e" + "uuid": "753f0297-4bff-49c8-b22a-1377e43a81f6" } }, "job_messages": [], @@ -1582,60 +1582,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "c02153e44a10e06a", + "id": "40769e0726e5d2f9", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "a3a16f375ef01612", + "id": "00e4fea3ca53d1d5", "src": "hda", - "uuid": "760d3bcc-0498-4f4a-9420-511468a0b0b3" + "uuid": "5cef395a-54ba-474b-b40b-1e5b3b2c4269" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "99e6c6e9665a5a56", + "id": "684375afe9650993", "src": "hda", - "uuid": "9836288d-70fb-464e-b565-90dc8f966379" + "uuid": "77cca133-2fb3-4cf3-b4b1-a802a1f09ea3" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "2d10fdf290562ab3", + "id": "45afc15ea654e191", "src": "hda", - "uuid": "cf0e5bca-9446-4574-b885-ab1636310493" + "uuid": "dbd53cde-61b2-4db8-b6bf-f0caaec76ace" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "071f312ace6db7aa", + "id": "8aa0c494b99ce49f", "src": "hda", - "uuid": "9e552d2e-e5f3-4163-b4b4-6351ec76f0d3" + "uuid": "8ea5339c-3186-4886-8af7-2a2d8134e161" }, "output_zip": { - "id": "72a012487a44f1a3", + "id": "4d559b2811c6a30e", "src": "hda", - "uuid": "a88370aa-4d36-4867-b0d6-613cc59ed01a" + "uuid": "800320dc-d181-40bf-b1cb-541f43a838c3" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpay0tme4v/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, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", + "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, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/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, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", + "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, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/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": "2025-05-16T12:38:53.803402", + "update_time": "2025-05-19T13:48:06.412363", "user_email": "planemo@galaxyproject.org", - "user_id": "a7025157dd5d3039" + "user_id": "fd8809ceca5b90d8" }, "status": "success", "test_index": 5, - "time_seconds": 52.96998858451843, + "time_seconds": 55.54361414909363, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" },