Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 8:07e902da89ad draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 09:23:51 +0000 |
| parents | 296e5145a862 |
| children | 0be569bd5443 |
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--- a/output.json Fri May 23 12:53:50 2025 +0000 +++ b/output.json Mon May 26 09:23:51 2025 +0000 @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "106ff655f8a511fe", + "id": "0a696a8b22798e06", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "8094a24bdbd328fd", + "id": "cb6d3fbb91be6861", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/b/1/1/dataset_b114952d-795f-4872-a508-1b68f71f6843.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/7/7/2/dataset_7728392b-6cec-4864-bb21-79c5330f34db.dat,/tmp/tmpulb7kecp/files/f/9/6/dataset_f96a1c6f-cc5b-4969-947e-d0c5d9bc1861.dat,/tmp/tmpulb7kecp/files/5/d/9/dataset_5d9fa39d-58a0-4385-a52a-cff566ab6569.dat,/tmp/tmpulb7kecp/files/9/2/d/dataset_92d74dbb-3200-4182-b1c1-b916d8b9636a.dat,/tmp/tmpulb7kecp/files/4/e/7/dataset_4e7f3975-e0c4-4043-a1d6-e798d43c88bd.dat,/tmp/tmpulb7kecp/files/9/6/5/dataset_965d5a1c-5b11-44c4-b1bc-392cb2e34bda.dat,/tmp/tmpulb7kecp/files/b/2/9/dataset_b29b6ede-fd7d-4db7-812a-e4719848c9d9.dat,/tmp/tmpulb7kecp/files/d/0/b/dataset_d0b8b55e-d329-4566-b8a2-8708f23d57d2.dat,/tmp/tmpulb7kecp/files/b/c/1/dataset_bc107665-0e38-42fe-8183-edb3b3f22248.dat,/tmp/tmpulb7kecp/files/f/7/e/dataset_f7e084da-7abc-4b0b-a75a-d7be088e30ee.dat,/tmp/tmpulb7kecp/files/6/2/e/dataset_62ece79d-c0cc-454a-bbd8-1c943ff0bcce.dat,/tmp/tmpulb7kecp/files/2/4/7/dataset_2476887f-77e7-4955-8e73-a0b57b50009d.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/7/7/2/dataset_7728392b-6cec-4864-bb21-79c5330f34db.dat:part_A.gb,/tmp/tmpulb7kecp/files/f/9/6/dataset_f96a1c6f-cc5b-4969-947e-d0c5d9bc1861.dat:part_B.gb,/tmp/tmpulb7kecp/files/5/d/9/dataset_5d9fa39d-58a0-4385-a52a-cff566ab6569.dat:part_C.gb,/tmp/tmpulb7kecp/files/9/2/d/dataset_92d74dbb-3200-4182-b1c1-b916d8b9636a.dat:part_D.gb,/tmp/tmpulb7kecp/files/4/e/7/dataset_4e7f3975-e0c4-4043-a1d6-e798d43c88bd.dat:part_E.gb,/tmp/tmpulb7kecp/files/9/6/5/dataset_965d5a1c-5b11-44c4-b1bc-392cb2e34bda.dat:part_F.gb,/tmp/tmpulb7kecp/files/b/2/9/dataset_b29b6ede-fd7d-4db7-812a-e4719848c9d9.dat:part_G.gb,/tmp/tmpulb7kecp/files/d/0/b/dataset_d0b8b55e-d329-4566-b8a2-8708f23d57d2.dat:part_H.gb,/tmp/tmpulb7kecp/files/b/c/1/dataset_bc107665-0e38-42fe-8183-edb3b3f22248.dat:part_I.gb,/tmp/tmpulb7kecp/files/f/7/e/dataset_f7e084da-7abc-4b0b-a75a-d7be088e30ee.dat:part_J.gb,/tmp/tmpulb7kecp/files/6/2/e/dataset_62ece79d-c0cc-454a-bbd8-1c943ff0bcce.dat:part_K.gb,/tmp/tmpulb7kecp/files/2/4/7/dataset_2476887f-77e7-4955-8e73-a0b57b50009d.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/tmpulb7kecp/job_working_directory/000/14/outputs/dataset_531b5c74-8577-4ba2-86cf-d8f25f16e169.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/b/a/a/dataset_baa59b14-7fb5-4efc-a75d-228d26b70adc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/14/outputs/dataset_49164d85-9bff-47f5-b8ee-de001d155fd3.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:13:12.978945", + "create_time": "2025-05-26T08:56:03.115650", "dependencies": [], "exit_code": 0, - "external_id": "178458", + "external_id": "78665", "galaxy_version": "24.2", "handler": null, - "history_id": "8094a24bdbd328fd", - "id": "a843aa6880d39864", + "history_id": "cb6d3fbb91be6861", + "id": "2ff5b0f6b4cfbb73", "inputs": { "assembly_csv": { - "id": "106ff655f8a511fe", + "id": "0a696a8b22798e06", "src": "hda", - "uuid": "b114952d-795f-4872-a508-1b68f71f6843" + "uuid": "baa59b14-7fb5-4efc-a75d-228d26b70adc" }, "genbank_files1": { - "id": "8094a24bdbd328fd", + "id": "cb6d3fbb91be6861", "src": "hda", - "uuid": "7728392b-6cec-4864-bb21-79c5330f34db" + "uuid": "f7bde375-2c6b-4e23-9117-e96bb4c3f6e6" }, "genbank_files10": { - "id": "54ed1ed3b165c7b4", + "id": "7ede2556a40dc9ba", "src": "hda", - "uuid": "f7e084da-7abc-4b0b-a75a-d7be088e30ee" + "uuid": "3217492e-bc97-4d61-87fd-b9d1f2e4534d" }, "genbank_files11": { - "id": "aa441ebc75addcb0", + "id": "76608081d307dc20", "src": "hda", - "uuid": "62ece79d-c0cc-454a-bbd8-1c943ff0bcce" + "uuid": "f8f04302-598c-4596-99a1-6c7d84b613d6" }, "genbank_files12": { - "id": "41108ccf3c813abd", + "id": "0551bf01e3dbca02", "src": "hda", - "uuid": "2476887f-77e7-4955-8e73-a0b57b50009d" + "uuid": "9f67cbfd-ca06-4926-b042-74a0d43b585a" }, "genbank_files2": { - "id": "6c2020bf7be1ec65", + "id": "18a1e53d7b8ec0fa", "src": "hda", - "uuid": "f96a1c6f-cc5b-4969-947e-d0c5d9bc1861" + "uuid": "ba5c9d10-e47e-4ced-9aaf-a51bf18e7932" }, "genbank_files3": { - "id": "8a7a2aba20929ed0", + "id": "afdf3d24f0e34eea", "src": "hda", - "uuid": "5d9fa39d-58a0-4385-a52a-cff566ab6569" + "uuid": "bf6e6482-afaa-4790-ac74-23f532fa48ad" }, "genbank_files4": { - "id": "53ad8e2eaf8a05d9", + "id": "285751a21c9d1d68", "src": "hda", - "uuid": "92d74dbb-3200-4182-b1c1-b916d8b9636a" + "uuid": "1b8c7b47-fdba-4046-953a-89dc0c07ae14" }, "genbank_files5": { - "id": "85b2c5efa0bce20f", + "id": "48e4779cf88cf124", "src": "hda", - "uuid": "4e7f3975-e0c4-4043-a1d6-e798d43c88bd" + "uuid": "5f5321b9-fa9a-4a73-9573-890d0c00209d" }, "genbank_files6": { - "id": "3758c7315f184c9a", + "id": "2bf3ecab9316a382", "src": "hda", - "uuid": "965d5a1c-5b11-44c4-b1bc-392cb2e34bda" + "uuid": "8557a762-7c36-4111-a015-2b61caad4e5b" }, "genbank_files7": { - "id": "cc5b73713462c207", + "id": "d51bf47fbc922335", "src": "hda", - "uuid": "b29b6ede-fd7d-4db7-812a-e4719848c9d9" + "uuid": "f7000fc2-7e04-4561-875c-b84614f51966" }, "genbank_files8": { - "id": "abedd81ff2360f10", + "id": "590bb56cc83504dc", "src": "hda", - "uuid": "d0b8b55e-d329-4566-b8a2-8708f23d57d2" + "uuid": "3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09" }, "genbank_files9": { - "id": "83d0643dcafc650b", + "id": "ff96e44e65db99f8", "src": "hda", - "uuid": "bc107665-0e38-42fe-8183-edb3b3f22248" + "uuid": "e3b26d77-5d05-4a0f-adf7-016bf86c5eb3" } }, "job_messages": [], @@ -108,60 +108,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "6c2020bf7be1ec65", + "id": "18a1e53d7b8ec0fa", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "03b30db777cad5e1", + "id": "be5466d8eb2c2229", "src": "hda", - "uuid": "21d43ad8-7969-4897-bade-2bde4913b7c5" + "uuid": "2c83aaa9-63df-43a5-b008-9a361a9fc312" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "d7483ddd36cf3921", + "id": "a37f81f30817f4ff", "src": "hda", - "uuid": "9420de76-fe00-401e-9cef-039d76b41e8f" + "uuid": "8ba2ce56-ba8b-4ff8-bcc0-54d0a2ad3b09" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "2239b1a77a4b659c", + "id": "b4705f371a43addc", "src": "hda", - "uuid": "e360b3e5-97c6-49be-9e0e-4ff44209fb03" + "uuid": "47741e71-6bf6-46ec-9353-25bb48d895ed" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "b9f6f443461a8e55", + "id": "0dc911fcb05967a3", "src": "hda", - "uuid": "580f1a4e-e43c-4396-9ae5-d441a0f64d1a" + "uuid": "6aa740ec-6985-4d66-8427-b1652fa06f3a" }, "output_zip": { - "id": "a843aa6880d39864", + "id": "2ff5b0f6b4cfbb73", "src": "hda", - "uuid": "531b5c74-8577-4ba2-86cf-d8f25f16e169" + "uuid": "49164d85-9bff-47f5-b8ee-de001d155fd3" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.78it/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.78it/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:13:26.150051", + "update_time": "2025-05-26T08:56:15.534051", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 0, - "time_seconds": 53.7402708530426, + "time_seconds": 54.95904994010925, "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": "9ebeb50920a3365f", + "id": "e01f0df21d75058c", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "8a7a2aba20929ed0", + "id": "afdf3d24f0e34eea", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/c/b/4/dataset_cb485986-3b87-4675-b3c5-cdb2d0287c2a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/a/6/0/dataset_a609f7c2-042e-4412-98a8-2056fe698533.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/a/6/0/dataset_a609f7c2-042e-4412-98a8-2056fe698533.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/tmpulb7kecp/job_working_directory/000/17/outputs/dataset_ff63bc11-8e44-4753-a248-329fb44ee3b1.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/b/2/dataset_5b2e01d9-e63b-45e1-8523-e88570aecbd1.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/17/outputs/dataset_81c8307a-8e03-4975-b3ec-1115f4f47284.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:13:37.414073", + "create_time": "2025-05-26T08:56:26.250368", "dependencies": [ { "cacheable": false, @@ -367,21 +367,21 @@ } ], "exit_code": 0, - "external_id": "178806", + "external_id": "79009", "galaxy_version": "24.2", "handler": null, - "history_id": "6c2020bf7be1ec65", - "id": "2239b1a77a4b659c", + "history_id": "18a1e53d7b8ec0fa", + "id": "b4705f371a43addc", "inputs": { "assembly_csv": { - "id": "9ebeb50920a3365f", + "id": "e01f0df21d75058c", "src": "hda", - "uuid": "cb485986-3b87-4675-b3c5-cdb2d0287c2a" + "uuid": "5b2e01d9-e63b-45e1-8523-e88570aecbd1" }, "genbank_files1": { - "id": "293d5da1ac833ef3", + "id": "bc8da7662961ae94", "src": "hda", - "uuid": "a609f7c2-042e-4412-98a8-2056fe698533" + "uuid": "5633084d-0123-48ba-b733-086550a95944" } }, "job_messages": [], @@ -392,55 +392,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "53ad8e2eaf8a05d9", + "id": "285751a21c9d1d68", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "a21f4c8cc3b535db", + "id": "d8c348e4a6c18790", "src": "hda", - "uuid": "0463b48d-c2d8-42a4-8b6a-ecb4dfc701c4" + "uuid": "39e12d2a-e4aa-491e-bb74-be0d48efaa36" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "c9bb032e1a0e8897", + "id": "cc98bdb1867cbf6a", "src": "hda", - "uuid": "89f175c4-8e96-49e3-8c45-514b2193b29a" + "uuid": "dbc568c1-dd73-4973-aa7a-f33cb279cbb7" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "68281df0cf338722", + "id": "dd60b22cea40a264", "src": "hda", - "uuid": "2a43a8fd-7b64-4f92-a483-6c716ec2f681" + "uuid": "3d0514f2-d798-484f-add3-d04103fef517" }, "output_zip": { - "id": "713969bb307bfc17", + "id": "cb5bc2d1019b090c", "src": "hda", - "uuid": "ff63bc11-8e44-4753-a248-329fb44ee3b1" + "uuid": "81c8307a-8e03-4975-b3ec-1115f4f47284" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.37it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.36it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/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, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.37it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.36it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/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, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:13:49.541469", + "update_time": "2025-05-26T08:56:38.283009", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 1, - "time_seconds": 23.19603419303894, + "time_seconds": 22.636474609375, "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": "6ba0e4a0e82495c8", + "id": "c6996082322986ef", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "85b2c5efa0bce20f", + "id": "48e4779cf88cf124", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/b/7/7/dataset_b7713227-6c97-4684-ac9a-76650631a0a9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/f/e/9/dataset_fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7.dat,/tmp/tmpulb7kecp/files/4/5/7/dataset_45763854-327e-472f-9cb3-a3cc72b8f76b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/f/e/9/dataset_fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpulb7kecp/files/4/5/7/dataset_45763854-327e-472f-9cb3-a3cc72b8f76b.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/tmpulb7kecp/job_working_directory/000/21/outputs/dataset_1d53129b-a396-429b-9971-2d00b993e48a.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/3/6/c/dataset_36c9642c-c980-4a5f-babe-e1140450965b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/21/outputs/dataset_dd39a396-84ad-4350-8d9b-a0efafd5ea2a.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:14:01.238952", + "create_time": "2025-05-26T08:56:49.662294", "dependencies": [ { "cacheable": false, @@ -646,26 +646,26 @@ } ], "exit_code": 0, - "external_id": "179225", + "external_id": "79436", "galaxy_version": "24.2", "handler": null, - "history_id": "8a7a2aba20929ed0", - "id": "713969bb307bfc17", + "history_id": "afdf3d24f0e34eea", + "id": "cb5bc2d1019b090c", "inputs": { "assembly_csv": { - "id": "6ba0e4a0e82495c8", + "id": "c6996082322986ef", "src": "hda", - "uuid": "b7713227-6c97-4684-ac9a-76650631a0a9" + "uuid": "36c9642c-c980-4a5f-babe-e1140450965b" }, "genbank_files1": { - "id": "f1fafc006c3c5be7", + "id": "ff6721ae641686bd", "src": "hda", - "uuid": "fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7" + "uuid": "fd7feec8-d839-4aac-ba59-54d4042d72d4" }, "genbank_files2": { - "id": "8c1f52fe6e59f5ac", + "id": "898f771988549b05", "src": "hda", - "uuid": "45763854-327e-472f-9cb3-a3cc72b8f76b" + "uuid": "097d3af5-48d7-4b15-9063-19cc11585d82" } }, "job_messages": [], @@ -676,40 +676,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "3758c7315f184c9a", + "id": "2bf3ecab9316a382", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "db12508970e81a14", + "id": "b995dfb8c32b92b7", "src": "hda", - "uuid": "1d53129b-a396-429b-9971-2d00b993e48a" + "uuid": "dd39a396-84ad-4350-8d9b-a0efafd5ea2a" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.37it/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, 2.23it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.37it/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, 2.23it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:14:13.046545", + "update_time": "2025-05-26T08:57:02.321903", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 2, - "time_seconds": 23.21994924545288, + "time_seconds": 23.856895685195923, "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": "a9ed9e5261104c2a", + "id": "9d9573fdc2182066", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { - "id": "cc5b73713462c207", + "id": "d51bf47fbc922335", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/5/1/3/dataset_513294c4-b1bf-4a02-a37d-6f4bd74436d9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/a/7/9/dataset_a79829ef-6450-404a-8d59-fa42ddb91ca3.dat,/tmp/tmpulb7kecp/files/7/c/7/dataset_7c74d4c3-38b5-40a7-9c71-482502e6e5f8.dat,/tmp/tmpulb7kecp/files/5/1/c/dataset_51c3184d-fd7e-49a8-af51-e29bbf7a8a37.dat,/tmp/tmpulb7kecp/files/2/4/4/dataset_24493579-a703-4b94-ac09-e283f59035b0.dat,/tmp/tmpulb7kecp/files/c/b/4/dataset_cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/a/7/9/dataset_a79829ef-6450-404a-8d59-fa42ddb91ca3.dat:GFP.gb,/tmp/tmpulb7kecp/files/7/c/7/dataset_7c74d4c3-38b5-40a7-9c71-482502e6e5f8.dat:p15A_kan.gb,/tmp/tmpulb7kecp/files/5/1/c/dataset_51c3184d-fd7e-49a8-af51-e29bbf7a8a37.dat:promoter.gb,/tmp/tmpulb7kecp/files/2/4/4/dataset_24493579-a703-4b94-ac09-e283f59035b0.dat:RFP.gb,/tmp/tmpulb7kecp/files/c/b/4/dataset_cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4.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/tmpulb7kecp/job_working_directory/000/28/outputs/dataset_47491132-901d-4249-9c1e-dfd12feae17e.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/2/5/1/dataset_251d413f-0fe8-42cd-8a76-7ef77cde6f15.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat:GFP.gb,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat:p15A_kan.gb,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat:promoter.gb,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat:RFP.gb,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/28/outputs/dataset_8e6b31eb-84b3-4184-92eb-33384ae50857.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:14:34.083682", + "create_time": "2025-05-26T08:57:24.342653", "dependencies": [ { "cacheable": false, @@ -915,41 +915,41 @@ } ], "exit_code": 0, - "external_id": "179816", + "external_id": "80040", "galaxy_version": "24.2", "handler": null, - "history_id": "53ad8e2eaf8a05d9", - "id": "db12508970e81a14", + "history_id": "285751a21c9d1d68", + "id": "b995dfb8c32b92b7", "inputs": { "assembly_csv": { - "id": "a9ed9e5261104c2a", + "id": "9d9573fdc2182066", "src": "hda", - "uuid": "513294c4-b1bf-4a02-a37d-6f4bd74436d9" + "uuid": "251d413f-0fe8-42cd-8a76-7ef77cde6f15" }, "genbank_files1": { - "id": "ce8e89b55ee6d12d", + "id": "241cfac882733d83", "src": "hda", - "uuid": "a79829ef-6450-404a-8d59-fa42ddb91ca3" + "uuid": "7d893bbf-b4e0-4d64-bafc-21ba1566237d" }, "genbank_files2": { - "id": "9c6b8acc292ccf30", + "id": "7ada2c781708b1e8", "src": "hda", - "uuid": "7c74d4c3-38b5-40a7-9c71-482502e6e5f8" + "uuid": "cc2314fa-924f-47c0-b89a-661fb78790a4" }, "genbank_files3": { - "id": "0b252ddd8f79f3ec", + "id": "4deb8a541e3f0671", "src": "hda", - "uuid": "51c3184d-fd7e-49a8-af51-e29bbf7a8a37" + "uuid": "8d097c97-7bd5-48eb-9f9e-f5b92ce19458" }, "genbank_files4": { - "id": "757270683c70cddd", + "id": "cdcc9004d7157de8", "src": "hda", - "uuid": "24493579-a703-4b94-ac09-e283f59035b0" + "uuid": "59189305-e832-4191-be7c-496c01c8aba6" }, "genbank_files5": { - "id": "3932a26d59be2681", + "id": "33fad5084f4d4cb5", "src": "hda", - "uuid": "cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4" + "uuid": "402500d7-6532-4008-9445-c0cf7fed5350" } }, "job_messages": [], @@ -960,40 +960,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "abedd81ff2360f10", + "id": "590bb56cc83504dc", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "8c26318d49002581", + "id": "4f510c4214d7d568", "src": "hda", - "uuid": "47491132-901d-4249-9c1e-dfd12feae17e" + "uuid": "8e6b31eb-84b3-4184-92eb-33384ae50857" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.05it/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.05it/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:14:44.485473", + "update_time": "2025-05-26T08:57:34.740635", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 3, - "time_seconds": 31.373873472213745, + "time_seconds": 32.283992767333984, "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": "723f42bbf157272d", + "id": "017df84d4155fcba", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "83d0643dcafc650b", + "id": "ff96e44e65db99f8", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/9/4/0/dataset_940a048a-ec9f-4cc9-9990-f0f1bb9c01db.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/d/5/9/dataset_d591902b-724d-446d-bad5-1ecf539f4193.dat,/tmp/tmpulb7kecp/files/4/5/7/dataset_457d680a-7fd5-42ce-8747-a78267083da9.dat,/tmp/tmpulb7kecp/files/1/a/9/dataset_1a9aa4c8-4387-4b65-a638-1033465060d7.dat,/tmp/tmpulb7kecp/files/3/f/e/dataset_3feea62b-c35b-4f65-937d-3233db6bf0ec.dat,/tmp/tmpulb7kecp/files/f/9/1/dataset_f917f42d-9d14-4b5e-aa4f-b04e06a56357.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/d/5/9/dataset_d591902b-724d-446d-bad5-1ecf539f4193.dat:BBa_E0040_GFP.gb,/tmp/tmpulb7kecp/files/4/5/7/dataset_457d680a-7fd5-42ce-8747-a78267083da9.dat:BBa_J23119_prom.gb,/tmp/tmpulb7kecp/files/1/a/9/dataset_1a9aa4c8-4387-4b65-a638-1033465060d7.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpulb7kecp/files/3/f/e/dataset_3feea62b-c35b-4f65-937d-3233db6bf0ec.dat:BBa_J61048_term.gb,/tmp/tmpulb7kecp/files/f/9/1/dataset_f917f42d-9d14-4b5e-aa4f-b04e06a56357.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/tmpulb7kecp/job_working_directory/000/35/outputs/dataset_332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/f/d/9/dataset_fd913c0f-ea98-4b8d-a170-961146c201d5.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat:BBa_E0040_GFP.gb,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat:BBa_J23119_prom.gb,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat:BBa_J23119_prom_flawed.gb,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat:BBa_J61048_term.gb,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/35/outputs/dataset_a3f2eab1-bbe1-401e-b436-b7ffc698ee3a.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:15:06.093194", + "create_time": "2025-05-26T08:57:56.917009", "dependencies": [ { "cacheable": false, @@ -1199,41 +1199,41 @@ } ], "exit_code": 0, - "external_id": "180435", + "external_id": "80672", "galaxy_version": "24.2", "handler": null, - "history_id": "85b2c5efa0bce20f", - "id": "8c26318d49002581", + "history_id": "48e4779cf88cf124", + "id": "4f510c4214d7d568", "inputs": { "assembly_csv": { - "id": "723f42bbf157272d", + "id": "017df84d4155fcba", "src": "hda", - "uuid": "940a048a-ec9f-4cc9-9990-f0f1bb9c01db" + "uuid": "fd913c0f-ea98-4b8d-a170-961146c201d5" }, "genbank_files1": { - "id": "068bcc8e8d7a762b", + "id": "1745fab1994e918a", "src": "hda", - "uuid": "d591902b-724d-446d-bad5-1ecf539f4193" + "uuid": "38402f39-a1d3-495e-afed-bf8335b4cdb6" }, "genbank_files2": { - "id": "9f11456f5a306175", + "id": "9f4b12edd1240647", "src": "hda", - "uuid": "457d680a-7fd5-42ce-8747-a78267083da9" + "uuid": "9c8ea453-16b9-4b9d-b171-9d5c0322adf9" }, "genbank_files3": { - "id": "4d6d92e009725c02", + "id": "070cf47a9114ebf0", "src": "hda", - "uuid": "1a9aa4c8-4387-4b65-a638-1033465060d7" + "uuid": "31a46fbb-0267-42e3-b9d3-c60804edd30c" }, "genbank_files4": { - "id": "ba31cade4e4f4bd8", + "id": "176efb58f023067c", "src": "hda", - "uuid": "3feea62b-c35b-4f65-937d-3233db6bf0ec" + "uuid": "e278e6ea-3146-49fa-a4f5-becf766e4f5e" }, "genbank_files5": { - "id": "5c13ba18dcd7e71d", + "id": "2c38922866e3bd19", "src": "hda", - "uuid": "f917f42d-9d14-4b5e-aa4f-b04e06a56357" + "uuid": "6a19d37f-54e1-4c94-a2b1-1a7f37820aad" } }, "job_messages": [], @@ -1244,55 +1244,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "54ed1ed3b165c7b4", + "id": "7ede2556a40dc9ba", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { - "id": "165ffecff174f921", + "id": "e9bea5372f4a6a20", "src": "hda", - "uuid": "dbf78ec4-1125-4869-b2c7-22ea1e088383" + "uuid": "80f480c8-264d-428b-8b95-253cd89d7764" }, "__new_primary_file_construct_gb|C2_gfp_term__": { - "id": "68b55cb1abb6ffc8", + "id": "1290d6537f2937e3", "src": "hda", - "uuid": "eefbb36b-1cb4-4159-a989-674ce4a361d9" + "uuid": "7b7b6524-575a-4dfc-800c-dc0d3e8ece79" }, "__new_primary_file_construct_gb|C3_final__": { - "id": "be504c8d89de9ae4", + "id": "cd293a8cb9d8e7b5", "src": "hda", - "uuid": "7c89fcf8-b98f-4719-bedc-509f7d2adbb8" + "uuid": "7be9e218-0841-46cd-ac62-5686969f6935" }, "output_zip": { - "id": "67dd2dff3a365063", + "id": "3651b2c7591f0e47", "src": "hda", - "uuid": "332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b" + "uuid": "a3f2eab1-bbe1-401e-b436-b7ffc698ee3a" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.89it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.55it/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, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.89it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.55it/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, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:15:19.591969", + "update_time": "2025-05-26T08:58:09.572798", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 4, - "time_seconds": 35.12441039085388, + "time_seconds": 34.93839716911316, "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": "8f56f36c2b9f0a7c", + "id": "b1a8f56fe428091e", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "aa441ebc75addcb0", + "id": "76608081d307dc20", "src": "hdca" }, "genbank_files": { - "id": "41108ccf3c813abd", + "id": "0551bf01e3dbca02", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/c/f/a/dataset_cfa1c628-1bad-4864-97c9-f5ff8ae3bb94.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/0/9/2/dataset_092e3d69-34a0-4c02-9593-859fa17016fb.dat,/tmp/tmpulb7kecp/files/e/d/5/dataset_ed59100d-a4e7-4eb8-9965-8817a8e44000.dat,/tmp/tmpulb7kecp/files/0/1/7/dataset_0172bdce-ca49-45d4-af2d-12a5304b55ca.dat,/tmp/tmpulb7kecp/files/d/2/2/dataset_d22475f3-6c2f-4c52-9164-12248ba5d2a8.dat,/tmp/tmpulb7kecp/files/1/d/9/dataset_1d9b3d4c-eed3-444e-87e6-29c04e915c0d.dat,/tmp/tmpulb7kecp/files/2/4/c/dataset_24c555ec-1536-4ef6-a07d-20d744f3b5fc.dat,/tmp/tmpulb7kecp/files/c/2/3/dataset_c23f475b-f826-4333-8641-66e68bfad42a.dat' --domesticated_seq '/tmp/tmpulb7kecp/files/f/f/a/dataset_ffa8dfa6-df34-412b-84ae-325a3e389a88.dat,/tmp/tmpulb7kecp/files/f/3/3/dataset_f33af6b6-cce3-49b2-a17e-9a168ad065f9.dat,/tmp/tmpulb7kecp/files/2/9/7/dataset_297ec6da-4e55-4534-94c7-903e7e107632.dat,/tmp/tmpulb7kecp/files/3/0/7/dataset_30785c7f-0628-4e63-be45-77272fdedb50.dat,/tmp/tmpulb7kecp/files/f/3/2/dataset_f32a9062-9cf7-48d9-9ddb-ef0c02526564.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/0/9/2/dataset_092e3d69-34a0-4c02-9593-859fa17016fb.dat:part_A.gb,/tmp/tmpulb7kecp/files/e/d/5/dataset_ed59100d-a4e7-4eb8-9965-8817a8e44000.dat:part_B.gb,/tmp/tmpulb7kecp/files/0/1/7/dataset_0172bdce-ca49-45d4-af2d-12a5304b55ca.dat:part_C.gb,/tmp/tmpulb7kecp/files/d/2/2/dataset_d22475f3-6c2f-4c52-9164-12248ba5d2a8.dat:part_D.gb,/tmp/tmpulb7kecp/files/1/d/9/dataset_1d9b3d4c-eed3-444e-87e6-29c04e915c0d.dat:part_E.gb,/tmp/tmpulb7kecp/files/2/4/c/dataset_24c555ec-1536-4ef6-a07d-20d744f3b5fc.dat:part_F.gb,/tmp/tmpulb7kecp/files/c/2/3/dataset_c23f475b-f826-4333-8641-66e68bfad42a.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpulb7kecp/files/f/f/a/dataset_ffa8dfa6-df34-412b-84ae-325a3e389a88.dat:part_H.gb,/tmp/tmpulb7kecp/files/f/3/3/dataset_f33af6b6-cce3-49b2-a17e-9a168ad065f9.dat:part_I.gb,/tmp/tmpulb7kecp/files/2/9/7/dataset_297ec6da-4e55-4534-94c7-903e7e107632.dat:part_J.gb,/tmp/tmpulb7kecp/files/3/0/7/dataset_30785c7f-0628-4e63-be45-77272fdedb50.dat:part_K.gb,/tmp/tmpulb7kecp/files/f/3/2/dataset_f32a9062-9cf7-48d9-9ddb-ef0c02526564.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/tmpulb7kecp/job_working_directory/000/49/outputs/dataset_da6f8b92-03ba-4561-81a4-2ac510aff8c6.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/9/7/b/dataset_97b16fa9-53ab-4e65-9de7-e30112bcdd06.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat' --domesticated_seq '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/49/outputs/dataset_2bca238e-5421-456d-bf98-1bd44e65fc76.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:16:00.836611", + "create_time": "2025-05-26T08:58:50.541909", "dependencies": [ { "cacheable": false, @@ -1502,76 +1502,76 @@ } ], "exit_code": 0, - "external_id": "181545", + "external_id": "81731", "galaxy_version": "24.2", "handler": null, - "history_id": "3758c7315f184c9a", - "id": "db168591f9c4d2a8", + "history_id": "2bf3ecab9316a382", + "id": "aa893e5f7beb4eb8", "inputs": { "assembly_csv": { - "id": "8f56f36c2b9f0a7c", + "id": "b1a8f56fe428091e", "src": "hda", - "uuid": "cfa1c628-1bad-4864-97c9-f5ff8ae3bb94" + "uuid": "97b16fa9-53ab-4e65-9de7-e30112bcdd06" }, "domesticated_input1": { - "id": "762d85be4105a0e7", + "id": "dbc527c8f70438a2", "src": "hda", - "uuid": "ffa8dfa6-df34-412b-84ae-325a3e389a88" + "uuid": "ef3f0423-f1dd-462b-8d68-e68cd6d59d82" }, "domesticated_input2": { - "id": "c453f926cdeee4bd", + "id": "a3ea165695c1e088", "src": "hda", - "uuid": "f33af6b6-cce3-49b2-a17e-9a168ad065f9" + "uuid": "ea297609-87c4-4bfc-abfd-084fbcc94d5b" }, "domesticated_input3": { - "id": "5bba4dfbf52e531c", + "id": "d4fcfbec208c480f", "src": "hda", - "uuid": "297ec6da-4e55-4534-94c7-903e7e107632" + "uuid": "60d919ff-9b54-4856-b3d0-9836114c2575" }, "domesticated_input4": { - "id": "58e4e52cefa9d689", + "id": "b53993d77cff267e", "src": "hda", - "uuid": "30785c7f-0628-4e63-be45-77272fdedb50" + "uuid": "08efef6d-13c4-4e1b-a155-859e0a0df989" }, "domesticated_input5": { - "id": "492cbe2cf83388c0", + "id": "e1a323c2b9a73ada", "src": "hda", - "uuid": "f32a9062-9cf7-48d9-9ddb-ef0c02526564" + "uuid": "e72facc2-0bd8-49e8-94e6-6b255853b030" }, "genbank_files1": { - "id": "5b9f36df99fe7ddd", + "id": "03a53f60ebb3b30b", "src": "hda", - "uuid": "092e3d69-34a0-4c02-9593-859fa17016fb" + "uuid": "823cfc4c-98db-494d-a03b-5181179a3581" }, "genbank_files2": { - "id": "83649da70bd4e994", + "id": "949b6e5fb08e3b2e", "src": "hda", - "uuid": "ed59100d-a4e7-4eb8-9965-8817a8e44000" + "uuid": "60a53b2c-927e-4c33-b6b0-2e927266044e" }, "genbank_files3": { - "id": "9e3a7410afb0cd47", + "id": "4b14363353165bd2", "src": "hda", - "uuid": "0172bdce-ca49-45d4-af2d-12a5304b55ca" + "uuid": "d357996d-45c3-4715-b8eb-ea6bb836b18e" }, "genbank_files4": { - "id": "db168591f9c4d2a8", + "id": "aa893e5f7beb4eb8", "src": "hda", - "uuid": "d22475f3-6c2f-4c52-9164-12248ba5d2a8" + "uuid": "dacfd7e2-f5ff-4821-8d70-f73307f7997e" }, "genbank_files5": { - "id": "fbc673f3c19d4e8f", + "id": "e33440187009b2c6", "src": "hda", - "uuid": "1d9b3d4c-eed3-444e-87e6-29c04e915c0d" + "uuid": "9b3f9357-c1cc-43c9-a81c-c100483b3a0d" }, "genbank_files6": { - "id": "612b3112dca3b89a", + "id": "ef97dc51810891e7", "src": "hda", - "uuid": "24c555ec-1536-4ef6-a07d-20d744f3b5fc" + "uuid": "5e43150c-3c7c-4072-9720-fdc085cd6d8b" }, "genbank_files7": { - "id": "1122563bf7246535", + "id": "16b078cfbe5cb4fb", "src": "hda", - "uuid": "c23f475b-f826-4333-8641-66e68bfad42a" + "uuid": "2de75a41-7673-4cef-aa63-2cf6d9466e8c" } }, "job_messages": [], @@ -1582,60 +1582,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "106ff655f8a511fe", + "id": "0a696a8b22798e06", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "4ec2fde3b391b5e9", + "id": "08065af9f1d51b0a", "src": "hda", - "uuid": "65c06a03-7919-4203-8aa0-ee2d6c747da3" + "uuid": "4837c85e-ba71-482d-91d1-be3e3179ee5a" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "db0ab281fdd171f3", + "id": "23c03036acf6de8c", "src": "hda", - "uuid": "00b0ee36-bed6-481a-8f87-a3ee2eb3c474" + "uuid": "a898af9c-3721-4b84-8ebc-790dc376316c" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "39bf58b498d37eb0", + "id": "950510fee01c22f4", "src": "hda", - "uuid": "c6fb815c-ee68-4263-9e77-86d27f1f5fd9" + "uuid": "be8dfa79-0421-418a-9822-af3e69e3bd0a" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "54d1dbb833355e05", + "id": "abd47de82fbecc4e", "src": "hda", - "uuid": "af82262d-217d-4952-8d8f-b733d902879c" + "uuid": "1455799d-9a0a-46e7-8ddb-df60f983fb53" }, "output_zip": { - "id": "7830aac4d222c450", + "id": "b52f373b44c22024", "src": "hda", - "uuid": "da6f8b92-03ba-4561-81a4-2ac510aff8c6" + "uuid": "2bca238e-5421-456d-bf98-1bd44e65fc76" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.43it/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", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.43it/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_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:16:13.850563", + "update_time": "2025-05-26T08:59:03.629936", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 5, - "time_seconds": 54.179964542388916, + "time_seconds": 53.84836268424988, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1647,21 +1647,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "a128918b334a087e", + "id": "4b6130eb686f10a7", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "a843aa6880d39864", + "id": "2ff5b0f6b4cfbb73", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/4/d/6/dataset_4d664c21-0606-48f2-a403-c970eada5469.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/b/f/7/dataset_bf78af79-2d13-4fd5-8858-a0fcf0527125.dat,/tmp/tmpulb7kecp/files/6/c/f/dataset_6cf6f59f-3cee-4539-85e2-0b5786b42a8a.dat,/tmp/tmpulb7kecp/files/8/c/1/dataset_8c1a4509-f793-4b1a-9fc2-599b836e6d1e.dat,/tmp/tmpulb7kecp/files/3/8/1/dataset_3818afb4-1184-43b1-aa48-13efabb7ecc8.dat,/tmp/tmpulb7kecp/files/9/0/e/dataset_90e377b6-c53e-4277-8c54-c361769ee52f.dat,/tmp/tmpulb7kecp/files/4/5/9/dataset_4594442a-8d2b-4f97-a280-8deb7915da9c.dat,/tmp/tmpulb7kecp/files/6/e/9/dataset_6e9767bf-085d-48d0-9ad3-596e435224f3.dat,/tmp/tmpulb7kecp/files/1/4/b/dataset_14bd369b-8410-484e-8402-33aac9998b84.dat,/tmp/tmpulb7kecp/files/1/1/8/dataset_1180d189-8f49-4811-8e79-957c7bf319e4.dat,/tmp/tmpulb7kecp/files/4/9/1/dataset_49140292-5bb2-4b2e-bf02-87402741d120.dat,/tmp/tmpulb7kecp/files/b/4/2/dataset_b4278d16-d56d-4cbf-8fc6-100f10a5a142.dat,/tmp/tmpulb7kecp/files/1/8/0/dataset_18021752-a186-4b63-ba68-b56da64c7e9a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/b/f/7/dataset_bf78af79-2d13-4fd5-8858-a0fcf0527125.dat:part_A.gb,/tmp/tmpulb7kecp/files/6/c/f/dataset_6cf6f59f-3cee-4539-85e2-0b5786b42a8a.dat:part_B.gb,/tmp/tmpulb7kecp/files/8/c/1/dataset_8c1a4509-f793-4b1a-9fc2-599b836e6d1e.dat:part_C.gb,/tmp/tmpulb7kecp/files/3/8/1/dataset_3818afb4-1184-43b1-aa48-13efabb7ecc8.dat:part_D.gb,/tmp/tmpulb7kecp/files/9/0/e/dataset_90e377b6-c53e-4277-8c54-c361769ee52f.dat:part_E.gb,/tmp/tmpulb7kecp/files/4/5/9/dataset_4594442a-8d2b-4f97-a280-8deb7915da9c.dat:part_F.gb,/tmp/tmpulb7kecp/files/6/e/9/dataset_6e9767bf-085d-48d0-9ad3-596e435224f3.dat:part_G.gb,/tmp/tmpulb7kecp/files/1/4/b/dataset_14bd369b-8410-484e-8402-33aac9998b84.dat:part_H.gb,/tmp/tmpulb7kecp/files/1/1/8/dataset_1180d189-8f49-4811-8e79-957c7bf319e4.dat:part_I.gb,/tmp/tmpulb7kecp/files/4/9/1/dataset_49140292-5bb2-4b2e-bf02-87402741d120.dat:part_J.gb,/tmp/tmpulb7kecp/files/b/4/2/dataset_b4278d16-d56d-4cbf-8fc6-100f10a5a142.dat:part_K.gb,/tmp/tmpulb7kecp/files/1/8/0/dataset_18021752-a186-4b63-ba68-b56da64c7e9a.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/tmpulb7kecp/job_working_directory/000/63/outputs/dataset_5e972ac3-a1c0-48c4-9db8-648343937891.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/0/4/dataset_5042213c-8bb6-48e0-9501-070e55a9a8c0.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/63/outputs/dataset_4e39f3b7-2899-410e-a32f-47270970ae14.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-23T12:16:53.743706", + "create_time": "2025-05-26T08:59:44.629082", "dependencies": [ { "cacheable": false, @@ -1841,76 +1841,76 @@ } ], "exit_code": 0, - "external_id": "182633", + "external_id": "82808", "galaxy_version": "24.2", "handler": null, - "history_id": "cc5b73713462c207", - "id": "54d1dbb833355e05", + "history_id": "d51bf47fbc922335", + "id": "abd47de82fbecc4e", "inputs": { "assembly_csv": { - "id": "a128918b334a087e", + "id": "4b6130eb686f10a7", "src": "hda", - "uuid": "4d664c21-0606-48f2-a403-c970eada5469" + "uuid": "5042213c-8bb6-48e0-9501-070e55a9a8c0" }, "domesticated_input1": { - "id": "7b8eadfe954993cc", + "id": "7c76f7472621b5d0", "src": "hda", - "uuid": "bf78af79-2d13-4fd5-8858-a0fcf0527125" + "uuid": "dd8d9744-d7f0-46ae-b26f-de961e3f5033" }, "domesticated_input10": { - "id": "eadce10583f118a6", + "id": "9bd6c123148263b6", "src": "hda", - "uuid": "49140292-5bb2-4b2e-bf02-87402741d120" + "uuid": "d2492f3b-8ea9-40e7-8bda-a15b506a22ac" }, "domesticated_input11": { - "id": "e9b288c32babea6b", + "id": "5d3d21e362e05995", "src": "hda", - "uuid": "b4278d16-d56d-4cbf-8fc6-100f10a5a142" + "uuid": "3a857675-027c-4b28-bf69-7591db569213" }, "domesticated_input12": { - "id": "e756934e84f08dfa", + "id": "043b0e9e9cf8c91c", "src": "hda", - "uuid": "18021752-a186-4b63-ba68-b56da64c7e9a" + "uuid": "26df2c50-4cbe-45f5-ba07-be8fb89cfb7c" }, "domesticated_input2": { - "id": "8437c985b2f2555c", + "id": "11e2d0eceb639139", "src": "hda", - "uuid": "6cf6f59f-3cee-4539-85e2-0b5786b42a8a" + "uuid": "aa64d9f2-f351-4776-aab6-648a5fa5f6da" }, "domesticated_input3": { - "id": "15bf1fabbf77770e", + "id": "991f793af87d39c4", "src": "hda", - "uuid": "8c1a4509-f793-4b1a-9fc2-599b836e6d1e" + "uuid": "1dbca58c-bd12-48c7-bbfe-49ef8801f8c3" }, "domesticated_input4": { - "id": "0892281234ec1188", + "id": "3429ba0772b9ca69", "src": "hda", - "uuid": "3818afb4-1184-43b1-aa48-13efabb7ecc8" + "uuid": "d396d7df-8e9d-441b-b04e-abaaa0c90a7f" }, "domesticated_input5": { - "id": "d9fb2dd412cb550f", + "id": "c04c164ed0056d43", "src": "hda", - "uuid": "90e377b6-c53e-4277-8c54-c361769ee52f" + "uuid": "4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a" }, "domesticated_input6": { - "id": "5448650c849fc11a", + "id": "b3ed12fa60bc840b", "src": "hda", - "uuid": "4594442a-8d2b-4f97-a280-8deb7915da9c" + "uuid": "2e907739-181d-44bc-8bc4-35d252e00535" }, "domesticated_input7": { - "id": "2f883fbbd5083370", + "id": "5406c597edc1a692", "src": "hda", - "uuid": "6e9767bf-085d-48d0-9ad3-596e435224f3" + "uuid": "9d3053e2-630d-4fba-9b08-09f59013ab96" }, "domesticated_input8": { - "id": "24d06ab2f2a935eb", + "id": "780d322efdca3fcd", "src": "hda", - "uuid": "14bd369b-8410-484e-8402-33aac9998b84" + "uuid": "26364877-f482-4b4d-8346-61a2f50f1ccf" }, "domesticated_input9": { - "id": "e5bc5fc4cffa052a", + "id": "951610fc65ac475f", "src": "hda", - "uuid": "1180d189-8f49-4811-8e79-957c7bf319e4" + "uuid": "6f64f828-be8e-4e72-a940-87396256fe3f" } }, "job_messages": [], @@ -1921,60 +1921,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "03b30db777cad5e1", + "id": "be5466d8eb2c2229", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "a0ee6696f34ccc35", + "id": "6d4b50576bf02b31", "src": "hda", - "uuid": "f59b0877-3920-4bb4-b968-f7ae54e3bec8" + "uuid": "d4f04f5f-16a6-4675-a892-fa6d05156592" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "f468d17a6d2490da", + "id": "550e95bf5471ae1d", "src": "hda", - "uuid": "b52ac80b-d674-4da6-8ff1-24842aac56e9" + "uuid": "845f0e19-1541-481b-a386-47135e8ebdf1" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "5d3f1c2fed018315", + "id": "359048b3278e74c9", "src": "hda", - "uuid": "400e46dc-92e4-418b-8f71-30a8ce7e1de7" + "uuid": "420b6912-da3c-4b75-ae88-b73f0c005864" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "b40e1d6349e0d9ca", + "id": "7a3e4925ca1f5f1d", "src": "hda", - "uuid": "03c7f474-9652-4786-954f-bd38c4f6b887" + "uuid": "5b639734-e44b-415c-b347-5a702df97945" }, "output_zip": { - "id": "652ce7490abe3672", + "id": "40a6167ab839cf08", "src": "hda", - "uuid": "5e972ac3-a1c0-48c4-9db8-648343937891" + "uuid": "4e39f3b7-2899-410e-a32f-47270970ae14" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", "genbank_files": null, "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.39it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/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, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.39it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/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, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-23T12:17:07.008117", + "update_time": "2025-05-26T08:59:57.832603", "user_email": "planemo@galaxyproject.org", - "user_id": "8094a24bdbd328fd" + "user_id": "cb6d3fbb91be6861" }, "status": "success", "test_index": 6, - "time_seconds": 53.04504728317261, + "time_seconds": 53.99832892417908, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" },