Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 7:296e5145a862 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Fri, 23 May 2025 12:53:50 +0000 |
| parents | e1e985913204 |
| children | 07e902da89ad |
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--- a/output.json Wed May 21 14:53:05 2025 +0000 +++ b/output.json Fri May 23 12:53:50 2025 +0000 @@ -1,7 +1,7 @@ { "summary": { "num_errors": 0, - "num_failures": 1, + "num_failures": 0, "num_skips": 0, "num_tests": 7 }, @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "acd1a5e1ec1673bf", + "id": "106ff655f8a511fe", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "9f2c11a06c2c8bb2", + "id": "8094a24bdbd328fd", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/a/5/7/dataset_a579429e-eabf-48bf-8baa-4b54e340af46.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/e/8/6/dataset_e86ad306-6960-4dec-80fb-023fa6da5227.dat,/tmp/tmpo3npfzdk/files/d/3/4/dataset_d340b2ee-f061-4028-8e61-c384afc4678a.dat,/tmp/tmpo3npfzdk/files/1/9/5/dataset_19569676-42b8-47f6-bb6d-fd8658cd6a37.dat,/tmp/tmpo3npfzdk/files/0/5/a/dataset_05a63af0-f9a3-42f0-8ba8-74359301395e.dat,/tmp/tmpo3npfzdk/files/c/6/3/dataset_c636704b-8f2a-4cb6-9b8c-17214dadb08d.dat,/tmp/tmpo3npfzdk/files/8/5/5/dataset_855d9062-afe1-48b7-a1e9-a499536155aa.dat,/tmp/tmpo3npfzdk/files/e/3/7/dataset_e37509ff-8016-49ce-a9ca-fb066a5b6be6.dat,/tmp/tmpo3npfzdk/files/e/d/d/dataset_edde499a-6247-4874-8ef6-921fa7d311b6.dat,/tmp/tmpo3npfzdk/files/6/6/c/dataset_66c4decf-8469-4302-8957-320e236c7ee7.dat,/tmp/tmpo3npfzdk/files/0/f/e/dataset_0fe1772a-d8b1-4b91-aee0-1a6d1577590e.dat,/tmp/tmpo3npfzdk/files/c/1/a/dataset_c1aa9b56-f155-44af-8af5-1997f3ae48a7.dat,/tmp/tmpo3npfzdk/files/2/7/1/dataset_27148f5e-d3f0-45b9-a5f6-90d12767b2af.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/e/8/6/dataset_e86ad306-6960-4dec-80fb-023fa6da5227.dat:part_A.gb,/tmp/tmpo3npfzdk/files/d/3/4/dataset_d340b2ee-f061-4028-8e61-c384afc4678a.dat:part_B.gb,/tmp/tmpo3npfzdk/files/1/9/5/dataset_19569676-42b8-47f6-bb6d-fd8658cd6a37.dat:part_C.gb,/tmp/tmpo3npfzdk/files/0/5/a/dataset_05a63af0-f9a3-42f0-8ba8-74359301395e.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/6/3/dataset_c636704b-8f2a-4cb6-9b8c-17214dadb08d.dat:part_E.gb,/tmp/tmpo3npfzdk/files/8/5/5/dataset_855d9062-afe1-48b7-a1e9-a499536155aa.dat:part_F.gb,/tmp/tmpo3npfzdk/files/e/3/7/dataset_e37509ff-8016-49ce-a9ca-fb066a5b6be6.dat:part_G.gb,/tmp/tmpo3npfzdk/files/e/d/d/dataset_edde499a-6247-4874-8ef6-921fa7d311b6.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/6/c/dataset_66c4decf-8469-4302-8957-320e236c7ee7.dat:part_I.gb,/tmp/tmpo3npfzdk/files/0/f/e/dataset_0fe1772a-d8b1-4b91-aee0-1a6d1577590e.dat:part_J.gb,/tmp/tmpo3npfzdk/files/c/1/a/dataset_c1aa9b56-f155-44af-8af5-1997f3ae48a7.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/7/1/dataset_27148f5e-d3f0-45b9-a5f6-90d12767b2af.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/tmpo3npfzdk/job_working_directory/000/14/outputs/dataset_d4a3a824-aae9-4493-811d-77a8abd69905.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:47:30.360925", + "create_time": "2025-05-23T12:13:12.978945", "dependencies": [], "exit_code": 0, - "external_id": "317822", + "external_id": "178458", "galaxy_version": "24.2", "handler": null, - "history_id": "9f2c11a06c2c8bb2", - "id": "18479e206f3c823f", + "history_id": "8094a24bdbd328fd", + "id": "a843aa6880d39864", "inputs": { "assembly_csv": { - "id": "acd1a5e1ec1673bf", + "id": "106ff655f8a511fe", "src": "hda", - "uuid": "a579429e-eabf-48bf-8baa-4b54e340af46" + "uuid": "b114952d-795f-4872-a508-1b68f71f6843" }, "genbank_files1": { - "id": "9f2c11a06c2c8bb2", + "id": "8094a24bdbd328fd", "src": "hda", - "uuid": "e86ad306-6960-4dec-80fb-023fa6da5227" + "uuid": "7728392b-6cec-4864-bb21-79c5330f34db" }, "genbank_files10": { - "id": "d905212b22d14b29", + "id": "54ed1ed3b165c7b4", "src": "hda", - "uuid": "0fe1772a-d8b1-4b91-aee0-1a6d1577590e" + "uuid": "f7e084da-7abc-4b0b-a75a-d7be088e30ee" }, "genbank_files11": { - "id": "64a027171405da09", + "id": "aa441ebc75addcb0", "src": "hda", - "uuid": "c1aa9b56-f155-44af-8af5-1997f3ae48a7" + "uuid": "62ece79d-c0cc-454a-bbd8-1c943ff0bcce" }, "genbank_files12": { - "id": "f3ab5b94869b932e", + "id": "41108ccf3c813abd", "src": "hda", - "uuid": "27148f5e-d3f0-45b9-a5f6-90d12767b2af" + "uuid": "2476887f-77e7-4955-8e73-a0b57b50009d" }, "genbank_files2": { - "id": "edba41b605a9f854", + "id": "6c2020bf7be1ec65", "src": "hda", - "uuid": "d340b2ee-f061-4028-8e61-c384afc4678a" + "uuid": "f96a1c6f-cc5b-4969-947e-d0c5d9bc1861" }, "genbank_files3": { - "id": "b1906c2e1f5de664", + "id": "8a7a2aba20929ed0", "src": "hda", - "uuid": "19569676-42b8-47f6-bb6d-fd8658cd6a37" + "uuid": "5d9fa39d-58a0-4385-a52a-cff566ab6569" }, "genbank_files4": { - "id": "d28b58e6679c5691", + "id": "53ad8e2eaf8a05d9", "src": "hda", - "uuid": "05a63af0-f9a3-42f0-8ba8-74359301395e" + "uuid": "92d74dbb-3200-4182-b1c1-b916d8b9636a" }, "genbank_files5": { - "id": "39de46ba349dfcbe", + "id": "85b2c5efa0bce20f", "src": "hda", - "uuid": "c636704b-8f2a-4cb6-9b8c-17214dadb08d" + "uuid": "4e7f3975-e0c4-4043-a1d6-e798d43c88bd" }, "genbank_files6": { - "id": "d10d7a9bf6c42600", + "id": "3758c7315f184c9a", "src": "hda", - "uuid": "855d9062-afe1-48b7-a1e9-a499536155aa" + "uuid": "965d5a1c-5b11-44c4-b1bc-392cb2e34bda" }, "genbank_files7": { - "id": "6f2e93d50b248cee", + "id": "cc5b73713462c207", "src": "hda", - "uuid": "e37509ff-8016-49ce-a9ca-fb066a5b6be6" + "uuid": "b29b6ede-fd7d-4db7-812a-e4719848c9d9" }, "genbank_files8": { - "id": "00a7ec1d542ff3f2", + "id": "abedd81ff2360f10", "src": "hda", - "uuid": "edde499a-6247-4874-8ef6-921fa7d311b6" + "uuid": "d0b8b55e-d329-4566-b8a2-8708f23d57d2" }, "genbank_files9": { - "id": "39eaa2809c3cd4cb", + "id": "83d0643dcafc650b", "src": "hda", - "uuid": "66c4decf-8469-4302-8957-320e236c7ee7" + "uuid": "bc107665-0e38-42fe-8183-edb3b3f22248" } }, "job_messages": [], @@ -108,60 +108,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "edba41b605a9f854", + "id": "6c2020bf7be1ec65", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "fae073f924dc0737", + "id": "03b30db777cad5e1", "src": "hda", - "uuid": "41fc11c8-e2d3-4dad-9886-b8b318d263b0" + "uuid": "21d43ad8-7969-4897-bade-2bde4913b7c5" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "a0099218a00b3fc6", + "id": "d7483ddd36cf3921", "src": "hda", - "uuid": "7bc46185-b70d-4e82-b1fe-e0bc1710c1c7" + "uuid": "9420de76-fe00-401e-9cef-039d76b41e8f" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "87b4cc5bde3d0d60", + "id": "2239b1a77a4b659c", "src": "hda", - "uuid": "79f1a377-2d26-4e23-aa72-01151870f643" + "uuid": "e360b3e5-97c6-49be-9e0e-4ff44209fb03" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "b1ff512a2804398b", + "id": "b9f6f443461a8e55", "src": "hda", - "uuid": "63ad38c1-369e-4ef2-b296-6c80774439a1" + "uuid": "580f1a4e-e43c-4396-9ae5-d441a0f64d1a" }, "output_zip": { - "id": "18479e206f3c823f", + "id": "a843aa6880d39864", "src": "hda", - "uuid": "d4a3a824-aae9-4493-811d-77a8abd69905" + "uuid": "531b5c74-8577-4ba2-86cf-d8f25f16e169" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/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, 2.42it/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, 1.79it/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, 2.43it/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", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/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, 2.43it/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_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-21T14:47:43.254778", + "update_time": "2025-05-23T12:13:26.150051", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 0, - "time_seconds": 52.45778512954712, + "time_seconds": 53.7402708530426, "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": "289d42720aa731f0", + "id": "9ebeb50920a3365f", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "b1906c2e1f5de664", + "id": "8a7a2aba20929ed0", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/e/c/2/dataset_ec2445f2-3c65-4da8-8eff-b766983bfc67.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/6/7/f/dataset_67f88938-ad76-4760-9f37-0ad6563677d2.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/6/7/f/dataset_67f88938-ad76-4760-9f37-0ad6563677d2.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/tmpo3npfzdk/job_working_directory/000/17/outputs/dataset_989e415d-7117-4c6a-9721-a471d4848b28.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:47:54.065116", + "create_time": "2025-05-23T12:13:37.414073", "dependencies": [ { "cacheable": false, @@ -367,21 +367,21 @@ } ], "exit_code": 0, - "external_id": "318162", + "external_id": "178806", "galaxy_version": "24.2", "handler": null, - "history_id": "edba41b605a9f854", - "id": "87b4cc5bde3d0d60", + "history_id": "6c2020bf7be1ec65", + "id": "2239b1a77a4b659c", "inputs": { "assembly_csv": { - "id": "289d42720aa731f0", + "id": "9ebeb50920a3365f", "src": "hda", - "uuid": "ec2445f2-3c65-4da8-8eff-b766983bfc67" + "uuid": "cb485986-3b87-4675-b3c5-cdb2d0287c2a" }, "genbank_files1": { - "id": "761015980e0fa5bb", + "id": "293d5da1ac833ef3", "src": "hda", - "uuid": "67f88938-ad76-4760-9f37-0ad6563677d2" + "uuid": "a609f7c2-042e-4412-98a8-2056fe698533" } }, "job_messages": [], @@ -392,55 +392,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "d28b58e6679c5691", + "id": "53ad8e2eaf8a05d9", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "250fdbecb1e4e593", + "id": "a21f4c8cc3b535db", "src": "hda", - "uuid": "20319120-7aa4-4a7b-8e21-e283565ebc51" + "uuid": "0463b48d-c2d8-42a4-8b6a-ecb4dfc701c4" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "b6d4ee56c656e869", + "id": "c9bb032e1a0e8897", "src": "hda", - "uuid": "ba35f878-8819-459e-acff-364b6393cd75" + "uuid": "89f175c4-8e96-49e3-8c45-514b2193b29a" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "d670a65869e0ee8d", + "id": "68281df0cf338722", "src": "hda", - "uuid": "646cac10-dab3-4b60-bb38-1a21ce52a0af" + "uuid": "2a43a8fd-7b64-4f92-a483-6c716ec2f681" }, "output_zip": { - "id": "3cd20c46fb8f3785", + "id": "713969bb307bfc17", "src": "hda", - "uuid": "989e415d-7117-4c6a-9721-a471d4848b28" + "uuid": "ff63bc11-8e44-4753-a248-329fb44ee3b1" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/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, 4.41it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.23it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.23it/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, 4.37it/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", "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, 4.41it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.23it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.23it/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, 4.37it/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_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-21T14:48:06.111506", + "update_time": "2025-05-23T12:13:49.541469", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 1, - "time_seconds": 22.7187819480896, + "time_seconds": 23.19603419303894, "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": "85c339cda4aedd7c", + "id": "6ba0e4a0e82495c8", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "39de46ba349dfcbe", + "id": "85b2c5efa0bce20f", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/f/8/e/dataset_f8e8f190-6448-4143-9c9d-318983554f6e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/f/0/d/dataset_f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d.dat,/tmp/tmpo3npfzdk/files/0/1/e/dataset_01ef92eb-7297-49ed-b933-21e2fd13abde.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/f/0/d/dataset_f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpo3npfzdk/files/0/1/e/dataset_01ef92eb-7297-49ed-b933-21e2fd13abde.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/tmpo3npfzdk/job_working_directory/000/21/outputs/dataset_27a350cf-f7f3-41f3-8b7d-a7f5a3857cda.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:48:17.296961", + "create_time": "2025-05-23T12:14:01.238952", "dependencies": [ { "cacheable": false, @@ -646,26 +646,26 @@ } ], "exit_code": 0, - "external_id": "318555", + "external_id": "179225", "galaxy_version": "24.2", "handler": null, - "history_id": "b1906c2e1f5de664", - "id": "3cd20c46fb8f3785", + "history_id": "8a7a2aba20929ed0", + "id": "713969bb307bfc17", "inputs": { "assembly_csv": { - "id": "85c339cda4aedd7c", + "id": "6ba0e4a0e82495c8", "src": "hda", - "uuid": "f8e8f190-6448-4143-9c9d-318983554f6e" + "uuid": "b7713227-6c97-4684-ac9a-76650631a0a9" }, "genbank_files1": { - "id": "65b6153cb018bc73", + "id": "f1fafc006c3c5be7", "src": "hda", - "uuid": "f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d" + "uuid": "fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7" }, "genbank_files2": { - "id": "bad7991cd53808a2", + "id": "8c1f52fe6e59f5ac", "src": "hda", - "uuid": "01ef92eb-7297-49ed-b933-21e2fd13abde" + "uuid": "45763854-327e-472f-9cb3-a3cc72b8f76b" } }, "job_messages": [], @@ -676,40 +676,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "d10d7a9bf6c42600", + "id": "3758c7315f184c9a", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "a6615d25b678d53d", + "id": "db12508970e81a14", "src": "hda", - "uuid": "27a350cf-f7f3-41f3-8b7d-a7f5a3857cda" + "uuid": "1d53129b-a396-429b-9971-2d00b993e48a" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/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, 2.35it/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, 2.37it/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, 2.35it/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, 2.37it/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": "2025-05-21T14:48:29.682156", + "update_time": "2025-05-23T12:14:13.046545", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 2, - "time_seconds": 23.41460394859314, + "time_seconds": 23.21994924545288, "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": "5685dbd0270421a3", + "id": "a9ed9e5261104c2a", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { - "id": "6f2e93d50b248cee", + "id": "cc5b73713462c207", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/2/e/b/dataset_2ebce83f-23bd-4ed9-bf81-84719ce47f36.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/b/a/9/dataset_ba9f3fda-e65a-4367-9883-988cf2a55bc7.dat,/tmp/tmpo3npfzdk/files/5/6/4/dataset_56477dbf-4a9f-4d85-8639-49bc05bff7b7.dat,/tmp/tmpo3npfzdk/files/7/5/d/dataset_75d82485-e3c8-4311-8952-658d8522f8a5.dat,/tmp/tmpo3npfzdk/files/f/a/f/dataset_faff73fe-2ef9-4c25-913c-df5e8b93306a.dat,/tmp/tmpo3npfzdk/files/8/5/9/dataset_859dcf3d-e0f7-4667-9c8d-9a9587d934fb.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/b/a/9/dataset_ba9f3fda-e65a-4367-9883-988cf2a55bc7.dat:GFP.gb,/tmp/tmpo3npfzdk/files/5/6/4/dataset_56477dbf-4a9f-4d85-8639-49bc05bff7b7.dat:p15A_kan.gb,/tmp/tmpo3npfzdk/files/7/5/d/dataset_75d82485-e3c8-4311-8952-658d8522f8a5.dat:promoter.gb,/tmp/tmpo3npfzdk/files/f/a/f/dataset_faff73fe-2ef9-4c25-913c-df5e8b93306a.dat:RFP.gb,/tmp/tmpo3npfzdk/files/8/5/9/dataset_859dcf3d-e0f7-4667-9c8d-9a9587d934fb.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/tmpo3npfzdk/job_working_directory/000/28/outputs/dataset_9a1970ad-354f-4dab-8065-2e37cd1d196b.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:48:51.044629", + "create_time": "2025-05-23T12:14:34.083682", "dependencies": [ { "cacheable": false, @@ -915,41 +915,41 @@ } ], "exit_code": 0, - "external_id": "319145", + "external_id": "179816", "galaxy_version": "24.2", "handler": null, - "history_id": "d28b58e6679c5691", - "id": "a6615d25b678d53d", + "history_id": "53ad8e2eaf8a05d9", + "id": "db12508970e81a14", "inputs": { "assembly_csv": { - "id": "5685dbd0270421a3", + "id": "a9ed9e5261104c2a", "src": "hda", - "uuid": "2ebce83f-23bd-4ed9-bf81-84719ce47f36" + "uuid": "513294c4-b1bf-4a02-a37d-6f4bd74436d9" }, "genbank_files1": { - "id": "78532c2c58a6724d", + "id": "ce8e89b55ee6d12d", "src": "hda", - "uuid": "ba9f3fda-e65a-4367-9883-988cf2a55bc7" + "uuid": "a79829ef-6450-404a-8d59-fa42ddb91ca3" }, "genbank_files2": { - "id": "6068244592d47240", + "id": "9c6b8acc292ccf30", "src": "hda", - "uuid": "56477dbf-4a9f-4d85-8639-49bc05bff7b7" + "uuid": "7c74d4c3-38b5-40a7-9c71-482502e6e5f8" }, "genbank_files3": { - "id": "f632d706e94b2046", + "id": "0b252ddd8f79f3ec", "src": "hda", - "uuid": "75d82485-e3c8-4311-8952-658d8522f8a5" + "uuid": "51c3184d-fd7e-49a8-af51-e29bbf7a8a37" }, "genbank_files4": { - "id": "3089f20183c33fb7", + "id": "757270683c70cddd", "src": "hda", - "uuid": "faff73fe-2ef9-4c25-913c-df5e8b93306a" + "uuid": "24493579-a703-4b94-ac09-e283f59035b0" }, "genbank_files5": { - "id": "b20d2aa5f122518a", + "id": "3932a26d59be2681", "src": "hda", - "uuid": "859dcf3d-e0f7-4667-9c8d-9a9587d934fb" + "uuid": "cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4" } }, "job_messages": [], @@ -960,40 +960,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "00a7ec1d542ff3f2", + "id": "abedd81ff2360f10", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "2accc8a350a16be5", + "id": "8c26318d49002581", "src": "hda", - "uuid": "9a1970ad-354f-4dab-8065-2e37cd1d196b" + "uuid": "47491132-901d-4249-9c1e-dfd12feae17e" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 48.44it/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, 49.05it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 48.44it/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, 49.05it/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": "2025-05-21T14:49:01.657843", + "update_time": "2025-05-23T12:14:44.485473", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 3, - "time_seconds": 32.04251265525818, + "time_seconds": 31.373873472213745, "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": "19069e20577e5aff", + "id": "723f42bbf157272d", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "39eaa2809c3cd4cb", + "id": "83d0643dcafc650b", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/1/d/4/dataset_1d489746-618d-43f9-ac80-377b4dd34b24.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/8/9/7/dataset_897a659b-ded6-4f1d-ae66-2a1cef19fe20.dat,/tmp/tmpo3npfzdk/files/7/4/c/dataset_74cd9512-f6fd-41db-8b25-6d9edd13fb35.dat,/tmp/tmpo3npfzdk/files/2/6/4/dataset_264baf3b-d201-449d-93bf-1408b04e3cc8.dat,/tmp/tmpo3npfzdk/files/b/8/7/dataset_b877c492-f532-4f4f-a95d-8dea0497c7ff.dat,/tmp/tmpo3npfzdk/files/f/a/1/dataset_fa14d755-6f98-4e94-9f24-cfbca2726e31.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/8/9/7/dataset_897a659b-ded6-4f1d-ae66-2a1cef19fe20.dat:BBa_E0040_GFP.gb,/tmp/tmpo3npfzdk/files/7/4/c/dataset_74cd9512-f6fd-41db-8b25-6d9edd13fb35.dat:BBa_J23119_prom.gb,/tmp/tmpo3npfzdk/files/2/6/4/dataset_264baf3b-d201-449d-93bf-1408b04e3cc8.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpo3npfzdk/files/b/8/7/dataset_b877c492-f532-4f4f-a95d-8dea0497c7ff.dat:BBa_J61048_term.gb,/tmp/tmpo3npfzdk/files/f/a/1/dataset_fa14d755-6f98-4e94-9f24-cfbca2726e31.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/tmpo3npfzdk/job_working_directory/000/35/outputs/dataset_ef294752-b154-44c3-828c-7165200df44d.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:49:23.080076", + "create_time": "2025-05-23T12:15:06.093194", "dependencies": [ { "cacheable": false, @@ -1199,41 +1199,41 @@ } ], "exit_code": 0, - "external_id": "319763", + "external_id": "180435", "galaxy_version": "24.2", "handler": null, - "history_id": "39de46ba349dfcbe", - "id": "2accc8a350a16be5", + "history_id": "85b2c5efa0bce20f", + "id": "8c26318d49002581", "inputs": { "assembly_csv": { - "id": "19069e20577e5aff", + "id": "723f42bbf157272d", "src": "hda", - "uuid": "1d489746-618d-43f9-ac80-377b4dd34b24" + "uuid": "940a048a-ec9f-4cc9-9990-f0f1bb9c01db" }, "genbank_files1": { - "id": "d016498c10e59856", + "id": "068bcc8e8d7a762b", "src": "hda", - "uuid": "897a659b-ded6-4f1d-ae66-2a1cef19fe20" + "uuid": "d591902b-724d-446d-bad5-1ecf539f4193" }, "genbank_files2": { - "id": "8ce5f5c286574bf4", + "id": "9f11456f5a306175", "src": "hda", - "uuid": "74cd9512-f6fd-41db-8b25-6d9edd13fb35" + "uuid": "457d680a-7fd5-42ce-8747-a78267083da9" }, "genbank_files3": { - "id": "b8e0a36ad3584e57", + "id": "4d6d92e009725c02", "src": "hda", - "uuid": "264baf3b-d201-449d-93bf-1408b04e3cc8" + "uuid": "1a9aa4c8-4387-4b65-a638-1033465060d7" }, "genbank_files4": { - "id": "14b4e4f7b248fbc1", + "id": "ba31cade4e4f4bd8", "src": "hda", - "uuid": "b877c492-f532-4f4f-a95d-8dea0497c7ff" + "uuid": "3feea62b-c35b-4f65-937d-3233db6bf0ec" }, "genbank_files5": { - "id": "773bba263401ee3f", + "id": "5c13ba18dcd7e71d", "src": "hda", - "uuid": "fa14d755-6f98-4e94-9f24-cfbca2726e31" + "uuid": "f917f42d-9d14-4b5e-aa4f-b04e06a56357" } }, "job_messages": [], @@ -1244,55 +1244,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "d905212b22d14b29", + "id": "54ed1ed3b165c7b4", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { - "id": "663fbeeba9821aac", + "id": "165ffecff174f921", "src": "hda", - "uuid": "17dc07bc-ee88-4d0a-914a-bd5e219c3c02" + "uuid": "dbf78ec4-1125-4869-b2c7-22ea1e088383" }, "__new_primary_file_construct_gb|C2_gfp_term__": { - "id": "522d7c5bcadc14e8", + "id": "68b55cb1abb6ffc8", "src": "hda", - "uuid": "9e3bf994-7926-4d59-8cba-2ea85e34d4c1" + "uuid": "eefbb36b-1cb4-4159-a989-674ce4a361d9" }, "__new_primary_file_construct_gb|C3_final__": { - "id": "092101d28c5662b8", + "id": "be504c8d89de9ae4", "src": "hda", - "uuid": "080209e3-58a5-4181-b460-bf02871b2f82" + "uuid": "7c89fcf8-b98f-4719-bedc-509f7d2adbb8" }, "output_zip": { - "id": "aa2a9c27c57d7b71", + "id": "67dd2dff3a365063", "src": "hda", - "uuid": "ef294752-b154-44c3-828c-7165200df44d" + "uuid": "332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/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, 1.92it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.56it/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, 1.89it/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", "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, 1.92it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.56it/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, 1.89it/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_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-21T14:49:36.465998", + "update_time": "2025-05-23T12:15:19.591969", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 4, - "time_seconds": 34.58101224899292, + "time_seconds": 35.12441039085388, "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": "79581be26281c6bb", + "id": "8f56f36c2b9f0a7c", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "64a027171405da09", + "id": "aa441ebc75addcb0", "src": "hdca" }, "genbank_files": { - "id": "f3ab5b94869b932e", + "id": "41108ccf3c813abd", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/8/c/c/dataset_8ccb55a4-733f-4671-a12c-c89cee5a694b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/5/8/6/dataset_586fc714-17c7-4356-a812-a25593d0b941.dat,/tmp/tmpo3npfzdk/files/f/7/5/dataset_f75d3cb4-8d11-4da3-99ae-56a96adeb45c.dat,/tmp/tmpo3npfzdk/files/0/f/2/dataset_0f2c03d7-84e9-4908-8cc2-ce94b456ad1d.dat,/tmp/tmpo3npfzdk/files/6/1/6/dataset_616f4db3-1967-47c9-b869-b02bcebad7c0.dat,/tmp/tmpo3npfzdk/files/5/b/4/dataset_5b4d9931-2f94-469f-8fbb-dddd1b4f23fe.dat,/tmp/tmpo3npfzdk/files/1/c/9/dataset_1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a.dat,/tmp/tmpo3npfzdk/files/1/5/6/dataset_156ffebe-1d63-442a-822e-94c26612aebb.dat' --domesticated_seq '/tmp/tmpo3npfzdk/files/a/3/2/dataset_a32d019a-ef10-42b8-92d3-b1a89149114e.dat,/tmp/tmpo3npfzdk/files/3/4/c/dataset_34ca3b9a-6d8e-4790-8e04-946f777aaa2f.dat,/tmp/tmpo3npfzdk/files/7/d/4/dataset_7d434fd6-3da6-4a35-a935-6262c2be3b95.dat,/tmp/tmpo3npfzdk/files/5/0/a/dataset_50a304a8-ff94-4efc-8d3c-9dd5714d0ab9.dat,/tmp/tmpo3npfzdk/files/d/4/7/dataset_d476b171-9eb3-4fcb-9e16-1d4631b211ae.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/5/8/6/dataset_586fc714-17c7-4356-a812-a25593d0b941.dat:part_A.gb,/tmp/tmpo3npfzdk/files/f/7/5/dataset_f75d3cb4-8d11-4da3-99ae-56a96adeb45c.dat:part_B.gb,/tmp/tmpo3npfzdk/files/0/f/2/dataset_0f2c03d7-84e9-4908-8cc2-ce94b456ad1d.dat:part_C.gb,/tmp/tmpo3npfzdk/files/6/1/6/dataset_616f4db3-1967-47c9-b869-b02bcebad7c0.dat:part_D.gb,/tmp/tmpo3npfzdk/files/5/b/4/dataset_5b4d9931-2f94-469f-8fbb-dddd1b4f23fe.dat:part_E.gb,/tmp/tmpo3npfzdk/files/1/c/9/dataset_1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a.dat:part_F.gb,/tmp/tmpo3npfzdk/files/1/5/6/dataset_156ffebe-1d63-442a-822e-94c26612aebb.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpo3npfzdk/files/a/3/2/dataset_a32d019a-ef10-42b8-92d3-b1a89149114e.dat:part_H.gb,/tmp/tmpo3npfzdk/files/3/4/c/dataset_34ca3b9a-6d8e-4790-8e04-946f777aaa2f.dat:part_I.gb,/tmp/tmpo3npfzdk/files/7/d/4/dataset_7d434fd6-3da6-4a35-a935-6262c2be3b95.dat:part_J.gb,/tmp/tmpo3npfzdk/files/5/0/a/dataset_50a304a8-ff94-4efc-8d3c-9dd5714d0ab9.dat:part_K.gb,/tmp/tmpo3npfzdk/files/d/4/7/dataset_d476b171-9eb3-4fcb-9e16-1d4631b211ae.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/tmpo3npfzdk/job_working_directory/000/49/outputs/dataset_26f09d54-6733-4b4f-9110-58b7422f6584.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:50:16.787614", + "create_time": "2025-05-23T12:16:00.836611", "dependencies": [ { "cacheable": false, @@ -1502,76 +1502,76 @@ } ], "exit_code": 0, - "external_id": "320811", + "external_id": "181545", "galaxy_version": "24.2", "handler": null, - "history_id": "d10d7a9bf6c42600", - "id": "056fda651c637916", + "history_id": "3758c7315f184c9a", + "id": "db168591f9c4d2a8", "inputs": { "assembly_csv": { - "id": "79581be26281c6bb", + "id": "8f56f36c2b9f0a7c", "src": "hda", - "uuid": "8ccb55a4-733f-4671-a12c-c89cee5a694b" + "uuid": "cfa1c628-1bad-4864-97c9-f5ff8ae3bb94" }, "domesticated_input1": { - "id": "85db74d9c0951b21", + "id": "762d85be4105a0e7", "src": "hda", - "uuid": "a32d019a-ef10-42b8-92d3-b1a89149114e" + "uuid": "ffa8dfa6-df34-412b-84ae-325a3e389a88" }, "domesticated_input2": { - "id": "1088aa990b0f6a3e", + "id": "c453f926cdeee4bd", "src": "hda", - "uuid": "34ca3b9a-6d8e-4790-8e04-946f777aaa2f" + "uuid": "f33af6b6-cce3-49b2-a17e-9a168ad065f9" }, "domesticated_input3": { - "id": "0adf69845d3170b2", + "id": "5bba4dfbf52e531c", "src": "hda", - "uuid": "7d434fd6-3da6-4a35-a935-6262c2be3b95" + "uuid": "297ec6da-4e55-4534-94c7-903e7e107632" }, "domesticated_input4": { - "id": "f38cba32d894e055", + "id": "58e4e52cefa9d689", "src": "hda", - "uuid": "50a304a8-ff94-4efc-8d3c-9dd5714d0ab9" + "uuid": "30785c7f-0628-4e63-be45-77272fdedb50" }, "domesticated_input5": { - "id": "d03e2be198c26beb", + "id": "492cbe2cf83388c0", "src": "hda", - "uuid": "d476b171-9eb3-4fcb-9e16-1d4631b211ae" + "uuid": "f32a9062-9cf7-48d9-9ddb-ef0c02526564" }, "genbank_files1": { - "id": "7f005c8d8137335e", + "id": "5b9f36df99fe7ddd", "src": "hda", - "uuid": "586fc714-17c7-4356-a812-a25593d0b941" + "uuid": "092e3d69-34a0-4c02-9593-859fa17016fb" }, "genbank_files2": { - "id": "2893678ebcfeac31", + "id": "83649da70bd4e994", "src": "hda", - "uuid": "f75d3cb4-8d11-4da3-99ae-56a96adeb45c" + "uuid": "ed59100d-a4e7-4eb8-9965-8817a8e44000" }, "genbank_files3": { - "id": "eebf6b53a0733527", + "id": "9e3a7410afb0cd47", "src": "hda", - "uuid": "0f2c03d7-84e9-4908-8cc2-ce94b456ad1d" + "uuid": "0172bdce-ca49-45d4-af2d-12a5304b55ca" }, "genbank_files4": { - "id": "056fda651c637916", + "id": "db168591f9c4d2a8", "src": "hda", - "uuid": "616f4db3-1967-47c9-b869-b02bcebad7c0" + "uuid": "d22475f3-6c2f-4c52-9164-12248ba5d2a8" }, "genbank_files5": { - "id": "554aac66b6b91c95", + "id": "fbc673f3c19d4e8f", "src": "hda", - "uuid": "5b4d9931-2f94-469f-8fbb-dddd1b4f23fe" + "uuid": "1d9b3d4c-eed3-444e-87e6-29c04e915c0d" }, "genbank_files6": { - "id": "e0b55cd244232b92", + "id": "612b3112dca3b89a", "src": "hda", - "uuid": "1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a" + "uuid": "24c555ec-1536-4ef6-a07d-20d744f3b5fc" }, "genbank_files7": { - "id": "5de07666a9f74c14", + "id": "1122563bf7246535", "src": "hda", - "uuid": "156ffebe-1d63-442a-822e-94c26612aebb" + "uuid": "c23f475b-f826-4333-8641-66e68bfad42a" } }, "job_messages": [], @@ -1582,60 +1582,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "acd1a5e1ec1673bf", + "id": "106ff655f8a511fe", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "bee5eb96186aeef0", + "id": "4ec2fde3b391b5e9", "src": "hda", - "uuid": "e0540e16-fb06-474f-9574-a0f8c8f44fae" + "uuid": "65c06a03-7919-4203-8aa0-ee2d6c747da3" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "19dda9511f29e82d", + "id": "db0ab281fdd171f3", "src": "hda", - "uuid": "3de1208e-5fa3-4899-b496-f1e4b8a69e8e" + "uuid": "00b0ee36-bed6-481a-8f87-a3ee2eb3c474" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "75d4ef21ebceb84b", + "id": "39bf58b498d37eb0", "src": "hda", - "uuid": "39adc107-3c51-4ceb-a401-d1e85b10d36c" + "uuid": "c6fb815c-ee68-4263-9e77-86d27f1f5fd9" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "7d27617ebf2a7ca2", + "id": "54d1dbb833355e05", "src": "hda", - "uuid": "5ff68ddd-6e45-47d3-877e-f0874370d1d7" + "uuid": "af82262d-217d-4952-8d8f-b733d902879c" }, "output_zip": { - "id": "aff3a7c3a5e84c2e", + "id": "7830aac4d222c450", "src": "hda", - "uuid": "26f09d54-6733-4b4f-9110-58b7422f6584" + "uuid": "da6f8b92-03ba-4561-81a4-2ac510aff8c6" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/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, 2.41it/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, 1.80it/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/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, 1.80it/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-21T14:50:29.418254", + "update_time": "2025-05-23T12:16:13.850563", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, "status": "success", "test_index": 5, - "time_seconds": 52.95538687705994, + "time_seconds": 54.179964542388916, "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": "1cfd8c9510cd79b8", + "id": "a128918b334a087e", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "18479e206f3c823f", + "id": "a843aa6880d39864", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/8/6/8/dataset_868edfc6-e59e-4522-bd0c-287140d27bcf.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat' --domesticated_seq '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat:part_A.gb,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat:part_B.gb,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat:part_C.gb,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat:part_E.gb,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat:part_F.gb,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat:part_G.gb,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat:part_I.gb,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat:part_J.gb,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat:part_L.gb' --file_name_mapping_dom '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat:part_A.gb,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat:part_B.gb,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat:part_C.gb,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat:part_E.gb,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat:part_F.gb,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat:part_G.gb,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat:part_I.gb,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat:part_J.gb,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.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/tmpo3npfzdk/job_working_directory/000/63/outputs/dataset_7ec4ccea-6d53-4d2c-b343-476013e8c0d9.dat'", + "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_version": "", "copied_from_job_id": null, - "create_time": "2025-05-21T14:51:10.356913", + "create_time": "2025-05-23T12:16:53.743706", "dependencies": [ { "cacheable": false, @@ -1840,148 +1840,80 @@ "version": "3.1.5" } ], - "exit_code": 1, - "external_id": "321954", + "exit_code": 0, + "external_id": "182633", "galaxy_version": "24.2", "handler": null, - "history_id": "6f2e93d50b248cee", - "id": "7d27617ebf2a7ca2", + "history_id": "cc5b73713462c207", + "id": "54d1dbb833355e05", "inputs": { "assembly_csv": { - "id": "1cfd8c9510cd79b8", + "id": "a128918b334a087e", "src": "hda", - "uuid": "868edfc6-e59e-4522-bd0c-287140d27bcf" + "uuid": "4d664c21-0606-48f2-a403-c970eada5469" }, "domesticated_input1": { - "id": "515ae798a3a66959", + "id": "7b8eadfe954993cc", "src": "hda", - "uuid": "4c7c671b-5fc3-4e96-b7f2-7e309d53588d" + "uuid": "bf78af79-2d13-4fd5-8858-a0fcf0527125" }, "domesticated_input10": { - "id": "ad6435740a2af171", + "id": "eadce10583f118a6", "src": "hda", - "uuid": "e6431634-077e-451e-afa3-b12c08fc5c7c" + "uuid": "49140292-5bb2-4b2e-bf02-87402741d120" }, "domesticated_input11": { - "id": "6d393a4d656a3907", + "id": "e9b288c32babea6b", "src": "hda", - "uuid": "758b4a45-c17d-4d1a-a289-79d3b2dfe524" + "uuid": "b4278d16-d56d-4cbf-8fc6-100f10a5a142" }, "domesticated_input12": { - "id": "b1f9d845e51287f2", + "id": "e756934e84f08dfa", "src": "hda", - "uuid": "226889a1-0543-4052-9d94-3276acdbd8ad" + "uuid": "18021752-a186-4b63-ba68-b56da64c7e9a" }, "domesticated_input2": { - "id": "24ad2b10f2de1c15", + "id": "8437c985b2f2555c", "src": "hda", - "uuid": "4c6b4c02-8f84-4314-8a13-682a855005e0" + "uuid": "6cf6f59f-3cee-4539-85e2-0b5786b42a8a" }, "domesticated_input3": { - "id": "6bd3728894d22921", + "id": "15bf1fabbf77770e", "src": "hda", - "uuid": "29c207fc-3958-40b7-8d3a-29486ebe729e" + "uuid": "8c1a4509-f793-4b1a-9fc2-599b836e6d1e" }, "domesticated_input4": { - "id": "a7fb62bdcc25db8f", + "id": "0892281234ec1188", "src": "hda", - "uuid": "c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c" + "uuid": "3818afb4-1184-43b1-aa48-13efabb7ecc8" }, "domesticated_input5": { - "id": "b4c6d612f8337c3c", + "id": "d9fb2dd412cb550f", "src": "hda", - "uuid": "cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd" + "uuid": "90e377b6-c53e-4277-8c54-c361769ee52f" }, "domesticated_input6": { - "id": "dac5f4fe4fc9d2c5", + "id": "5448650c849fc11a", "src": "hda", - "uuid": "eb6733f2-ea91-4ce2-878c-0bca789bfe95" + "uuid": "4594442a-8d2b-4f97-a280-8deb7915da9c" }, "domesticated_input7": { - "id": "01a8e5946ae7b883", + "id": "2f883fbbd5083370", "src": "hda", - "uuid": "dea7a300-b098-41a1-863d-ec55e3b78bda" + "uuid": "6e9767bf-085d-48d0-9ad3-596e435224f3" }, "domesticated_input8": { - "id": "348481ce28d8892f", + "id": "24d06ab2f2a935eb", "src": "hda", - "uuid": "13300353-8b8d-4bd4-9d25-88dceda7594b" + "uuid": "14bd369b-8410-484e-8402-33aac9998b84" }, "domesticated_input9": { - "id": "c53526ace39ecb75", - "src": "hda", - "uuid": "61ffb7d6-856a-4e4a-9da3-48a419455e92" - }, - "genbank_files1": { - "id": "515ae798a3a66959", - "src": "hda", - "uuid": "4c7c671b-5fc3-4e96-b7f2-7e309d53588d" - }, - "genbank_files10": { - "id": "ad6435740a2af171", - "src": "hda", - "uuid": "e6431634-077e-451e-afa3-b12c08fc5c7c" - }, - "genbank_files11": { - "id": "6d393a4d656a3907", - "src": "hda", - "uuid": "758b4a45-c17d-4d1a-a289-79d3b2dfe524" - }, - "genbank_files12": { - "id": "b1f9d845e51287f2", - "src": "hda", - "uuid": "226889a1-0543-4052-9d94-3276acdbd8ad" - }, - "genbank_files2": { - "id": "24ad2b10f2de1c15", - "src": "hda", - "uuid": "4c6b4c02-8f84-4314-8a13-682a855005e0" - }, - "genbank_files3": { - "id": "6bd3728894d22921", + "id": "e5bc5fc4cffa052a", "src": "hda", - "uuid": "29c207fc-3958-40b7-8d3a-29486ebe729e" - }, - "genbank_files4": { - "id": "a7fb62bdcc25db8f", - "src": "hda", - "uuid": "c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c" - }, - "genbank_files5": { - "id": "b4c6d612f8337c3c", - "src": "hda", - "uuid": "cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd" - }, - "genbank_files6": { - "id": "dac5f4fe4fc9d2c5", - "src": "hda", - "uuid": "eb6733f2-ea91-4ce2-878c-0bca789bfe95" - }, - "genbank_files7": { - "id": "01a8e5946ae7b883", - "src": "hda", - "uuid": "dea7a300-b098-41a1-863d-ec55e3b78bda" - }, - "genbank_files8": { - "id": "348481ce28d8892f", - "src": "hda", - "uuid": "13300353-8b8d-4bd4-9d25-88dceda7594b" - }, - "genbank_files9": { - "id": "c53526ace39ecb75", - "src": "hda", - "uuid": "61ffb7d6-856a-4e4a-9da3-48a419455e92" + "uuid": "1180d189-8f49-4811-8e79-957c7bf319e4" } }, - "job_messages": [ - { - "code_desc": "", - "desc": "Fatal error: Exit code 1 ()", - "error_level": 3, - "exit_code": 1, - "type": "exit_code" - } - ], + "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", @@ -1989,45 +1921,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "fae073f924dc0737", + "id": "03b30db777cad5e1", "src": "hdca" } }, "outputs": { + "__new_primary_file_construct_gb|construct_1__": { + "id": "a0ee6696f34ccc35", + "src": "hda", + "uuid": "f59b0877-3920-4bb4-b968-f7ae54e3bec8" + }, + "__new_primary_file_construct_gb|construct_2__": { + "id": "f468d17a6d2490da", + "src": "hda", + "uuid": "b52ac80b-d674-4da6-8ff1-24842aac56e9" + }, + "__new_primary_file_construct_gb|construct_3__": { + "id": "5d3f1c2fed018315", + "src": "hda", + "uuid": "400e46dc-92e4-418b-8f71-30a8ce7e1de7" + }, + "__new_primary_file_construct_gb|construct_4__": { + "id": "b40e1d6349e0d9ca", + "src": "hda", + "uuid": "03c7f474-9652-4786-954f-bd38c4f6b887" + }, "output_zip": { - "id": "24ef522ceac5a910", + "id": "652ce7490abe3672", "src": "hda", - "uuid": "7ec4ccea-6d53-4d2c-b343-476013e8c0d9" + "uuid": "5e972ac3-a1c0-48c4-9db8-648343937891" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", - "genbank_files": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", + "genbank_files": null, "topology": "\"circular\"" }, - "state": "error", - "stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n", - "stdout": "", + "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", + "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": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n", - "tool_stdout": "", - "update_time": "2025-05-21T14:51:18.877985", + "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_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", "user_email": "planemo@galaxyproject.org", - "user_id": "9f2c11a06c2c8bb2" + "user_id": "8094a24bdbd328fd" }, - "output_problems": [ - "Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n.", - "Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 22, in cloning_simulation\n repository.import_records(files=domesticated_files,\n ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n use_file_names_as_ids=use_file_names_as_id,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n topology=topology)\n ^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n self.add_records(records, collection=collection)\n ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n self.add_record(record, collection=collection)\n ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in in repo\n.", - "Output collection 'construct_gb': expected to have 4 elements, but it had 0." - ], - "status": "failure", + "status": "success", "test_index": 6, - "time_seconds": 49.28661274909973, + "time_seconds": 53.04504728317261, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" },