Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 3:044d36066cb3 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Fri, 16 May 2025 12:40:59 +0000 |
| parents | dc450979fcd4 |
| children | 254d284a5be9 |
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--- a/output.json Fri May 16 11:32:06 2025 +0000 +++ b/output.json Fri May 16 12:40:59 2025 +0000 @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "a2e8f3fd1611e7f5", + "id": "c02153e44a10e06a", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "1d1943aa60deb628", + "id": "a7025157dd5d3039", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/6/a/4/dataset_6a407f29-14a2-4358-8781-97a5a60006bf.dat,/tmp/tmps36anksu/files/9/c/0/dataset_9c05120b-2a93-4298-a718-2db482dec9e0.dat,/tmp/tmps36anksu/files/e/9/d/dataset_e9dd6c4a-5d1c-48d6-b072-bb67929590f5.dat,/tmp/tmps36anksu/files/c/2/a/dataset_c2a67b9c-bd0d-483b-b229-1f396bc8c275.dat,/tmp/tmps36anksu/files/5/3/d/dataset_53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00.dat,/tmp/tmps36anksu/files/4/0/f/dataset_40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0.dat,/tmp/tmps36anksu/files/1/4/b/dataset_14b815cb-038e-4836-bb4e-3f049395271c.dat,/tmp/tmps36anksu/files/3/2/7/dataset_32719970-8009-4818-a623-ba980af84d70.dat,/tmp/tmps36anksu/files/6/8/e/dataset_68e30a2d-a44d-40e6-a619-efa1e8cd6e4b.dat,/tmp/tmps36anksu/files/2/3/c/dataset_23c06fae-96cc-4ff8-9e23-111139ce1a92.dat,/tmp/tmps36anksu/files/d/2/9/dataset_d29c16a7-2470-418e-a8f1-1da7c5372dde.dat,/tmp/tmps36anksu/files/2/9/0/dataset_290bfdf4-f595-42f1-a2f0-0f9a9d8e71df.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/4/2/0/dataset_420c4b07-ea17-4e63-9f48-4cc364e28432.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/6/a/4/dataset_6a407f29-14a2-4358-8781-97a5a60006bf.dat:part_A.gb,/tmp/tmps36anksu/files/9/c/0/dataset_9c05120b-2a93-4298-a718-2db482dec9e0.dat:part_B.gb,/tmp/tmps36anksu/files/e/9/d/dataset_e9dd6c4a-5d1c-48d6-b072-bb67929590f5.dat:part_C.gb,/tmp/tmps36anksu/files/c/2/a/dataset_c2a67b9c-bd0d-483b-b229-1f396bc8c275.dat:part_D.gb,/tmp/tmps36anksu/files/5/3/d/dataset_53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00.dat:part_E.gb,/tmp/tmps36anksu/files/4/0/f/dataset_40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0.dat:part_F.gb,/tmp/tmps36anksu/files/1/4/b/dataset_14b815cb-038e-4836-bb4e-3f049395271c.dat:part_G.gb,/tmp/tmps36anksu/files/3/2/7/dataset_32719970-8009-4818-a623-ba980af84d70.dat:part_H.gb,/tmp/tmps36anksu/files/6/8/e/dataset_68e30a2d-a44d-40e6-a619-efa1e8cd6e4b.dat:part_I.gb,/tmp/tmps36anksu/files/2/3/c/dataset_23c06fae-96cc-4ff8-9e23-111139ce1a92.dat:part_J.gb,/tmp/tmps36anksu/files/d/2/9/dataset_d29c16a7-2470-418e-a8f1-1da7c5372dde.dat:part_K.gb,/tmp/tmps36anksu/files/2/9/0/dataset_290bfdf4-f595-42f1-a2f0-0f9a9d8e71df.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/14/outputs/dataset_19827d46-96d8-48c8-b434-17f9e4732aec.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/a/5/2/dataset_a522972a-c994-4ec0-a130-e3e1e101d126.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat:part_A.gb,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat:part_B.gb,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat:part_C.gb,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat:part_D.gb,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat:part_E.gb,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat:part_F.gb,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat:part_G.gb,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat:part_H.gb,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat:part_I.gb,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat:part_J.gb,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat:part_K.gb,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmph0r87skq/job_working_directory/000/14/outputs/dataset_109d2ac1-716e-4c47-a2b9-25e9d68cd9b7.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T08:54:45.629427", + "create_time": "2025-05-16T12:35:55.635805", "dependencies": [], "exit_code": 0, - "external_id": "69472", + "external_id": "205109", "galaxy_version": "24.2", "handler": null, - "history_id": "1d1943aa60deb628", - "id": "306d449b91ecb0a3", + "history_id": "a7025157dd5d3039", + "id": "d49d8be9932a8ee0", "inputs": { "assembly_csv": { - "id": "a2e8f3fd1611e7f5", + "id": "c02153e44a10e06a", "src": "hda", - "uuid": "420c4b07-ea17-4e63-9f48-4cc364e28432" + "uuid": "a522972a-c994-4ec0-a130-e3e1e101d126" }, "genbank_files1": { - "id": "1d1943aa60deb628", + "id": "a7025157dd5d3039", "src": "hda", - "uuid": "6a407f29-14a2-4358-8781-97a5a60006bf" + "uuid": "eb40ee5e-5155-4303-9230-94926c63daaf" }, "genbank_files10": { - "id": "b55875807068e59e", + "id": "26800a0030991202", "src": "hda", - "uuid": "23c06fae-96cc-4ff8-9e23-111139ce1a92" + "uuid": "184d9904-3705-424e-b3f7-e5b7b773880f" }, "genbank_files11": { - "id": "4b64a67f616af776", + "id": "9e9c740782c078df", "src": "hda", - "uuid": "d29c16a7-2470-418e-a8f1-1da7c5372dde" + "uuid": "4a10d392-6ebc-413c-bd71-db425aa1aa0a" }, "genbank_files12": { - "id": "1fda217ac9617c88", + "id": "d70a40a14f24deac", "src": "hda", - "uuid": "290bfdf4-f595-42f1-a2f0-0f9a9d8e71df" + "uuid": "835878c6-84f1-465c-b34e-d177885e567d" }, "genbank_files2": { - "id": "13a3899f03fff34a", + "id": "ce87194f2a532da8", "src": "hda", - "uuid": "9c05120b-2a93-4298-a718-2db482dec9e0" + "uuid": "4a9a1335-c528-438d-b80a-62b9608dbade" }, "genbank_files3": { - "id": "6872e1ad22eb2e5d", + "id": "e52e8d0a017d5bd2", "src": "hda", - "uuid": "e9dd6c4a-5d1c-48d6-b072-bb67929590f5" + "uuid": "7caa4f6a-a734-461f-ac38-c95442632c5a" }, "genbank_files4": { - "id": "248d7f69d2402068", + "id": "4dd0eedec5562f6e", "src": "hda", - "uuid": "c2a67b9c-bd0d-483b-b229-1f396bc8c275" + "uuid": "93127db8-2409-4544-93e5-6243a6d253ef" }, "genbank_files5": { - "id": "a363c57bce5ddac4", + "id": "d1cbd0905c1fc860", "src": "hda", - "uuid": "53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00" + "uuid": "e292919e-0a9a-403a-aa6b-30aa552881bd" }, "genbank_files6": { - "id": "8ab843ac4a5890da", + "id": "0494b81690cb2f5c", "src": "hda", - "uuid": "40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0" + "uuid": "4a7c1e6b-f470-414e-b533-7390f74a64fc" }, "genbank_files7": { - "id": "6206f91299006d13", + "id": "edce0bc0654ca8cc", "src": "hda", - "uuid": "14b815cb-038e-4836-bb4e-3f049395271c" + "uuid": "7f3df904-0bc5-456a-8679-cc58d06e214e" }, "genbank_files8": { - "id": "278f145ab0478700", + "id": "052d0d471d180256", "src": "hda", - "uuid": "32719970-8009-4818-a623-ba980af84d70" + "uuid": "a605738c-9b6d-44c6-891e-01cb729ea4dc" }, "genbank_files9": { - "id": "84aedadb70ef205b", + "id": "5827a0347340e98b", "src": "hda", - "uuid": "68e30a2d-a44d-40e6-a619-efa1e8cd6e4b" + "uuid": "10c35405-af25-41d3-9dbd-a411b4b65b98" } }, "job_messages": [], @@ -106,37 +106,62 @@ "job_stderr": "", "job_stdout": "", "model_class": "Job", - "output_collections": {}, + "output_collections": { + "construct_gb": { + "id": "ce87194f2a532da8", + "src": "hdca" + } + }, "outputs": { + "__new_primary_file_construct_gb|construct_1__": { + "id": "68bcb17f47b988de", + "src": "hda", + "uuid": "2c9a5458-38f0-4591-bb2d-452aac86ce0b" + }, + "__new_primary_file_construct_gb|construct_2__": { + "id": "7cb8b41737d3d7aa", + "src": "hda", + "uuid": "026f0937-350b-4ae7-96da-1e685237a8c8" + }, + "__new_primary_file_construct_gb|construct_3__": { + "id": "e558db6e0f20f34c", + "src": "hda", + "uuid": "df750e5d-b2f4-43f1-bf95-aa0d980bb98a" + }, + "__new_primary_file_construct_gb|construct_4__": { + "id": "87544afc708050c8", + "src": "hda", + "uuid": "0ba9a694-1b4e-4ff4-b6f2-87503d04cd66" + }, "output_zip": { - "id": "306d449b91ecb0a3", + "id": "d49d8be9932a8ee0", "src": "hda", - "uuid": "19827d46-96d8-48c8-b434-17f9e4732aec" + "uuid": "109d2ac1-716e-4c47-a2b9-25e9d68cd9b7" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmph0r87skq/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, 2.38it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/s, now=None]\r \r", + "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, 2.38it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", - "update_time": "2025-05-16T08:54:59.050276", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", + "update_time": "2025-05-16T12:36:09.065234", "user_email": "planemo@galaxyproject.org", - "user_id": "1d1943aa60deb628" + "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 0, - "time_seconds": 53.80709099769592, + "time_seconds": 54.82133865356445, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -148,21 +173,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "343611dad2e145e6", + "id": "13b114ac662002c6", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "13a3899f03fff34a", + "id": "e52e8d0a017d5bd2", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/5/c/2/dataset_5c2150b5-537a-4971-98ef-959bb4141fac.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/7/a/0/dataset_7a09a16a-a7f7-44ce-8e1d-5f6baf385c44.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmps36anksu/files/5/c/2/dataset_5c2150b5-537a-4971-98ef-959bb4141fac.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/17/outputs/dataset_4c70b3f9-9fb4-4e1c-942c-47fd78a5a348.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/5/7/9/dataset_579b13e6-f14d-401c-88ee-b25ed3bf42dc.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmph0r87skq/job_working_directory/000/17/outputs/dataset_36e0457f-1da8-456a-86c9-20ea242688bc.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T08:55:10.522461", + "create_time": "2025-05-16T12:36:19.661290", "dependencies": [ { "cacheable": false, @@ -180,7 +205,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", @@ -202,7 +227,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", @@ -224,7 +249,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", @@ -246,7 +271,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", @@ -268,7 +293,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", @@ -290,7 +315,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", @@ -312,7 +337,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", @@ -334,29 +359,29 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", - "version": "3.1.4" + "version": "3.1.5" } ], "exit_code": 0, - "external_id": "69816", + "external_id": "205459", "galaxy_version": "24.2", "handler": null, - "history_id": "13a3899f03fff34a", - "id": "6fff2cd3fd6e4947", + "history_id": "ce87194f2a532da8", + "id": "e558db6e0f20f34c", "inputs": { "assembly_csv": { - "id": "343611dad2e145e6", + "id": "13b114ac662002c6", "src": "hda", - "uuid": "7a09a16a-a7f7-44ce-8e1d-5f6baf385c44" + "uuid": "579b13e6-f14d-401c-88ee-b25ed3bf42dc" }, "genbank_files1": { - "id": "03c59a54410e4ccf", + "id": "16385471cc722641", "src": "hda", - "uuid": "5c2150b5-537a-4971-98ef-959bb4141fac" + "uuid": "f2e8406c-fdb7-4b30-aa74-202b93292a26" } }, "job_messages": [], @@ -365,37 +390,57 @@ "job_stderr": "", "job_stdout": "", "model_class": "Job", - "output_collections": {}, + "output_collections": { + "construct_gb": { + "id": "4dd0eedec5562f6e", + "src": "hdca" + } + }, "outputs": { + "__new_primary_file_construct_gb|construct_1__": { + "id": "eb4747fb10762624", + "src": "hda", + "uuid": "8b9f07c0-2a2f-49db-b0b9-e3b27b5d2102" + }, + "__new_primary_file_construct_gb|construct_2__": { + "id": "fa2c1cd7e40ca607", + "src": "hda", + "uuid": "694f0f93-1c26-4a8b-91ed-bcb7fe4b3784" + }, + "__new_primary_file_construct_gb|construct_3__": { + "id": "2c9180ba70391455", + "src": "hda", + "uuid": "e57dc6e8-10e6-4527-a375-9ed583735c59" + }, "output_zip": { - "id": "6fff2cd3fd6e4947", + "id": "cf8958f7b0d14fa5", "src": "hda", - "uuid": "4c70b3f9-9fb4-4e1c-942c-47fd78a5a348" + "uuid": "36e0457f-1da8-456a-86c9-20ea242688bc" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", + "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, 4.10it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.10it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.09it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.38it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_assembly_plan.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/construct_3_connections_graph.pdf\nassambly_simulation/construct_3/provided_parts_records/Frag_5b.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_4c.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_2.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1_connections_graph.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_2.gb\nassambly_simulation/part_records/Frag_5.gb\nassambly_simulation/part_records/Frag_5b.gb\nassambly_simulation/part_records/Frag_4.gb\nassambly_simulation/part_records/Frag_4c.gb\nassambly_simulation/part_records/Frag_4b.gb\nassambly_simulation/part_records/Frag_3.gb\nassambly_simulation/part_records/Frag_1.gb\nassambly_simulation/part_records/Frag_2.gb\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2_connections_graph.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_5/error.csv\nassambly_simulation/construct_5/construct_5_connections_graph.pdf\nassambly_simulation/construct_5/warnings.csv\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4b_01.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4b.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_5/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/construct_4_connections_graph.pdf\nassambly_simulation/construct_4/error.csv\nassambly_simulation/construct_4/warnings.csv\nassambly_simulation/construct_4/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_4/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_4_01.pdf\n", + "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/s, now=None]\r \r", + "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, 4.10it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.10it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.09it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.38it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_assembly_plan.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/construct_3_connections_graph.pdf\nassambly_simulation/construct_3/provided_parts_records/Frag_5b.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_4c.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_3/provided_parts_records/Frag_2.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1_connections_graph.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_1/provided_parts_records/Frag_2.gb\nassambly_simulation/part_records/Frag_5.gb\nassambly_simulation/part_records/Frag_5b.gb\nassambly_simulation/part_records/Frag_4.gb\nassambly_simulation/part_records/Frag_4c.gb\nassambly_simulation/part_records/Frag_4b.gb\nassambly_simulation/part_records/Frag_3.gb\nassambly_simulation/part_records/Frag_1.gb\nassambly_simulation/part_records/Frag_2.gb\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2_connections_graph.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/provided_parts_records/Frag_5.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_2/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_5/error.csv\nassambly_simulation/construct_5/construct_5_connections_graph.pdf\nassambly_simulation/construct_5/warnings.csv\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4_01.pdf\nassambly_simulation/construct_5/fragments_in_construct_5_homology_mix/Frag_4b_01.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4b.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_5/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_5/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_4b.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_5/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/construct_4_connections_graph.pdf\nassambly_simulation/construct_4/error.csv\nassambly_simulation/construct_4/warnings.csv\nassambly_simulation/construct_4/provided_parts_plots/Frag_4.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_3.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_2.pdf\nassambly_simulation/construct_4/provided_parts_plots/Frag_1.pdf\nassambly_simulation/construct_4/provided_parts_records/Frag_4.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_3.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_1.gb\nassambly_simulation/construct_4/provided_parts_records/Frag_2.gb\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_1_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_2_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_3_01.pdf\nassambly_simulation/construct_4/fragments_in_construct_4_homology_mix/Frag_4_01.pdf\n", - "update_time": "2025-05-16T08:55:23.301357", + "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", + "update_time": "2025-05-16T12:36:31.612352", "user_email": "planemo@galaxyproject.org", - "user_id": "1d1943aa60deb628" + "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 1, - "time_seconds": 24.055506706237793, + "time_seconds": 22.601666688919067, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -407,21 +452,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "eae50b1e0ba0bca8", + "id": "84906eb14284db27", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "6872e1ad22eb2e5d", + "id": "d1cbd0905c1fc860", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/a/a/0/dataset_aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2.dat,/tmp/tmps36anksu/files/4/b/b/dataset_4bb2bf6a-b351-4a80-ab47-d4d56aefa38c.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/5/a/f/dataset_5af89b00-757d-4606-b6c8-d00d3f0ca39e.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/a/a/0/dataset_aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmps36anksu/files/4/b/b/dataset_4bb2bf6a-b351-4a80-ab47-d4d56aefa38c.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/21/outputs/dataset_bd5c88b9-1efd-4507-b875-13dfebff9d6a.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/2/0/e/dataset_20eb88b1-0fc5-476b-a409-da7f598780b6.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmph0r87skq/job_working_directory/000/21/outputs/dataset_0ffdda24-b80f-4db5-8c10-1467d34eb3a8.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T08:55:35.420052", + "create_time": "2025-05-16T12:36:42.888728", "dependencies": [ { "cacheable": false, @@ -439,7 +484,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", @@ -461,7 +506,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", @@ -483,7 +528,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", @@ -505,7 +550,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", @@ -527,7 +572,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", @@ -549,7 +594,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", @@ -571,7 +616,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", @@ -593,34 +638,34 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", - "version": "3.1.4" + "version": "3.1.5" } ], "exit_code": 0, - "external_id": "70205", + "external_id": "205894", "galaxy_version": "24.2", "handler": null, - "history_id": "6872e1ad22eb2e5d", - "id": "8205956dbdec438f", + "history_id": "e52e8d0a017d5bd2", + "id": "cf8958f7b0d14fa5", "inputs": { "assembly_csv": { - "id": "eae50b1e0ba0bca8", + "id": "84906eb14284db27", "src": "hda", - "uuid": "5af89b00-757d-4606-b6c8-d00d3f0ca39e" + "uuid": "20eb88b1-0fc5-476b-a409-da7f598780b6" }, "genbank_files1": { - "id": "e685210c6961cf21", + "id": "1fdafe0e70c0e721", "src": "hda", - "uuid": "aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2" + "uuid": "15741680-9963-4b3d-979e-792be37256f2" }, "genbank_files2": { - "id": "fb0119a6d133c713", + "id": "044728be18fd1186", "src": "hda", - "uuid": "4bb2bf6a-b351-4a80-ab47-d4d56aefa38c" + "uuid": "d3de76b3-3793-46fa-990e-970e1bcb2a72" } }, "job_messages": [], @@ -629,37 +674,42 @@ "job_stderr": "", "job_stdout": "", "model_class": "Job", - "output_collections": {}, + "output_collections": { + "construct_gb": { + "id": "0494b81690cb2f5c", + "src": "hdca" + } + }, "outputs": { "output_zip": { - "id": "8205956dbdec438f", + "id": "920c0db56b0a806b", "src": "hda", - "uuid": "bd5c88b9-1efd-4507-b875-13dfebff9d6a" + "uuid": "0ffdda24-b80f-4db5-8c10-1467d34eb3a8" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", + "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, 2.34it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/Construct2_flawed/Construct2_flawed_connections_graph.pdf\nassambly_simulation/Construct2_flawed/error.csv\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10268_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10244_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10281_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10232_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10233_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10233.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10232.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10244.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10268.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10281.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct2_flawed/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10233.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10232.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10268.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10281.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10244.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p4_sfGFP-part1.gb\nassambly_simulation/Construct1/error.csv\nassambly_simulation/Construct1/Construct1_connections_graph.pdf\nassambly_simulation/Construct1/warnings.csv\nassambly_simulation/Construct1/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct1/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct1/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct1/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p4_sfGFP-part1.gb\n", + "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.42it/s, now=None]\r \r", + "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, 2.34it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_warnings.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assambly_summary.csv\nassambly_simulation/Construct2_flawed/Construct2_flawed_connections_graph.pdf\nassambly_simulation/Construct2_flawed/error.csv\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10268_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10244_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10281_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10232_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/RFP_GFP_BO_10233_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct2_flawed/fragments_in_Construct2_flawed_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10233.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10232.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10244.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10268.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/RFP_GFP_BO_10281.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct2_flawed/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct2_flawed/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10233.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10232.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10268.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10281.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/RFP_GFP_BO_10244.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct2_flawed/provided_parts_records/p4_sfGFP-part1.gb\nassambly_simulation/Construct1/error.csv\nassambly_simulation/Construct1/Construct1_connections_graph.pdf\nassambly_simulation/Construct1/warnings.csv\nassambly_simulation/Construct1/provided_parts_plots/p4_sfGFP-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p6_sfGFP-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p1_mRFP1-part1.pdf\nassambly_simulation/Construct1/provided_parts_plots/p3_mRFP1-part3.pdf\nassambly_simulation/Construct1/provided_parts_plots/p2_mRFP1-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p5_sfGFP-part2.pdf\nassambly_simulation/Construct1/provided_parts_plots/p7_backbone.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p1_mRFP1-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p3_mRFP1-part3_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p7_backbone_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p4_sfGFP-part1_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p5_sfGFP-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p2_mRFP1-part2_01.pdf\nassambly_simulation/Construct1/fragments_in_Construct1_homology_mix/p6_sfGFP-part3_01.pdf\nassambly_simulation/Construct1/provided_parts_records/p5_sfGFP-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p6_sfGFP-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p2_mRFP1-part2.gb\nassambly_simulation/Construct1/provided_parts_records/p1_mRFP1-part1.gb\nassambly_simulation/Construct1/provided_parts_records/p7_backbone.gb\nassambly_simulation/Construct1/provided_parts_records/p3_mRFP1-part3.gb\nassambly_simulation/Construct1/provided_parts_records/p4_sfGFP-part1.gb\n", - "update_time": "2025-05-16T08:55:47.617074", + "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.42it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "update_time": "2025-05-16T12:36:54.097489", "user_email": "planemo@galaxyproject.org", - "user_id": "1d1943aa60deb628" + "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 2, - "time_seconds": 24.352636098861694, + "time_seconds": 22.133039951324463, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -671,123 +721,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "c4d206bede85e5c1", + "id": "df13d5ca39cba7c4", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { - "id": "248d7f69d2402068", + "id": "edce0bc0654ca8cc", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/0/9/d/dataset_09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2.dat,/tmp/tmps36anksu/files/b/e/6/dataset_be63c5f6-6c15-43c9-a467-0f00c3395bcf.dat,/tmp/tmps36anksu/files/2/e/0/dataset_2e03930b-3e9f-45be-9750-42560f39cf14.dat,/tmp/tmps36anksu/files/5/b/d/dataset_5bdbe27f-640f-4db1-bc7b-fcedf4b2737a.dat,/tmp/tmps36anksu/files/c/d/5/dataset_cd53d85a-7ced-4da5-bc73-eb4b74a200e3.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/e/d/3/dataset_ed3f4797-0002-46e3-a245-70ec97e59118.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmps36anksu/files/0/9/d/dataset_09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2.dat:GFP.gb,/tmp/tmps36anksu/files/b/e/6/dataset_be63c5f6-6c15-43c9-a467-0f00c3395bcf.dat:p15A_kan.gb,/tmp/tmps36anksu/files/2/e/0/dataset_2e03930b-3e9f-45be-9750-42560f39cf14.dat:promoter.gb,/tmp/tmps36anksu/files/5/b/d/dataset_5bdbe27f-640f-4db1-bc7b-fcedf4b2737a.dat:RFP.gb,/tmp/tmps36anksu/files/c/d/5/dataset_cd53d85a-7ced-4da5-bc73-eb4b74a200e3.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/28/outputs/dataset_2ce9e85d-d4e7-4104-833f-9fcac95e2c6d.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/e/9/7/dataset_e971a6cf-b13e-4a65-a78d-aa22a0ea1fff.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat:GFP.gb,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat:p15A_kan.gb,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat:promoter.gb,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat:RFP.gb,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmph0r87skq/job_working_directory/000/28/outputs/dataset_5e0faa51-141c-49d1-ba84-ca8aba27508c.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T08:56:09.388287", - "dependencies": [], - "exit_code": 0, - "external_id": "70839", - "galaxy_version": "24.2", - "handler": null, - "history_id": "248d7f69d2402068", - "id": "ecaf8d4d1aeb8c86", - "inputs": { - "assembly_csv": { - "id": "c4d206bede85e5c1", - "src": "hda", - "uuid": "ed3f4797-0002-46e3-a245-70ec97e59118" - }, - "genbank_files1": { - "id": "065a19c3622776e9", - "src": "hda", - "uuid": "09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2" - }, - "genbank_files2": { - "id": "ac67f4a6521db48c", - "src": "hda", - "uuid": "be63c5f6-6c15-43c9-a467-0f00c3395bcf" - }, - "genbank_files3": { - "id": "77ed38528f61eafd", - "src": "hda", - "uuid": "2e03930b-3e9f-45be-9750-42560f39cf14" - }, - "genbank_files4": { - "id": "626b9fd2eae5943c", - "src": "hda", - "uuid": "5bdbe27f-640f-4db1-bc7b-fcedf4b2737a" - }, - "genbank_files5": { - "id": "4a4771cb4e71e8ed", - "src": "hda", - "uuid": "cd53d85a-7ced-4da5-bc73-eb4b74a200e3" - } - }, - "job_messages": [], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output_zip": { - "id": "ecaf8d4d1aeb8c86", - "src": "hda", - "uuid": "2ce9e85d-d4e7-4104-833f-9fcac95e2c6d" - } - }, - "params": { - "__input_ext": "\"input\"", - "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", - "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "dbkey": "\"?\"", - "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 4, \"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, 49.95it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_cancelled_assemblies.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/LMA-S/error.csv\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_fwd.pdf\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_adapter.pdf\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_adapter.gb\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_fwd.gb\nassambly_simulation/L2RBS-xS/error.csv\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_adapter.pdf\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_fwd.pdf\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_fwd.gb\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_adapter.gb\nassambly_simulation/L1RBS-xS/error.csv\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_adapter.pdf\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_fwd.pdf\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_fwd.gb\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_adapter.gb\nassambly_simulation/LMB-P/error.csv\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_adapter.pdf\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_fwd.pdf\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_fwd.gb\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_adapter.gb\nassambly_simulation/L1RBS-1P/error.csv\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_fwd.pdf\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_adapter.pdf\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_adapter.gb\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_fwd.gb\nassambly_simulation/L2RBS-1P/error.csv\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_fwd.pdf\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_adapter.pdf\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_adapter.gb\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_fwd.gb\nassambly_simulation/LMA-P/error.csv\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_fwd.pdf\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_adapter.pdf\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_fwd.gb\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_adapter.gb\nassambly_simulation/LMB-S/error.csv\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_fwd.pdf\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_adapter.pdf\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_fwd.gb\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_adapter.gb\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, 49.95it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assambly_cancelled_assemblies.csv\nassambly_simulation/assambly_errors.csv\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/LMA-S/error.csv\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_fwd.pdf\nassambly_simulation/LMA-S/provided_parts_plots/LMA-S_adapter.pdf\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_adapter.gb\nassambly_simulation/LMA-S/provided_parts_records/LMA-S_fwd.gb\nassambly_simulation/L2RBS-xS/error.csv\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_adapter.pdf\nassambly_simulation/L2RBS-xS/provided_parts_plots/L2RBS-xS_fwd.pdf\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_fwd.gb\nassambly_simulation/L2RBS-xS/provided_parts_records/L2RBS-xS_adapter.gb\nassambly_simulation/L1RBS-xS/error.csv\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_adapter.pdf\nassambly_simulation/L1RBS-xS/provided_parts_plots/L1RBS-xS_fwd.pdf\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_fwd.gb\nassambly_simulation/L1RBS-xS/provided_parts_records/L1RBS-xS_adapter.gb\nassambly_simulation/LMB-P/error.csv\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_adapter.pdf\nassambly_simulation/LMB-P/provided_parts_plots/LMB-P_fwd.pdf\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_fwd.gb\nassambly_simulation/LMB-P/provided_parts_records/LMB-P_adapter.gb\nassambly_simulation/L1RBS-1P/error.csv\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_fwd.pdf\nassambly_simulation/L1RBS-1P/provided_parts_plots/L1RBS-1P_adapter.pdf\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_adapter.gb\nassambly_simulation/L1RBS-1P/provided_parts_records/L1RBS-1P_fwd.gb\nassambly_simulation/L2RBS-1P/error.csv\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_fwd.pdf\nassambly_simulation/L2RBS-1P/provided_parts_plots/L2RBS-1P_adapter.pdf\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_adapter.gb\nassambly_simulation/L2RBS-1P/provided_parts_records/L2RBS-1P_fwd.gb\nassambly_simulation/LMA-P/error.csv\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_fwd.pdf\nassambly_simulation/LMA-P/provided_parts_plots/LMA-P_adapter.pdf\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_fwd.gb\nassambly_simulation/LMA-P/provided_parts_records/LMA-P_adapter.gb\nassambly_simulation/LMB-S/error.csv\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_fwd.pdf\nassambly_simulation/LMB-S/provided_parts_plots/LMB-S_adapter.pdf\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_fwd.gb\nassambly_simulation/LMB-S/provided_parts_records/LMB-S_adapter.gb\n", - "update_time": "2025-05-16T08:56:20.015826", - "user_email": "planemo@galaxyproject.org", - "user_id": "1d1943aa60deb628" - }, - "status": "success", - "test_index": 3, - "time_seconds": 32.09558367729187, - "tool_id": "cloning_simulation", - "tool_version": "0.1.0+galaxy0" - }, - "has_data": true, - "id": "cloning_simulation-3" - }, - { - "data": { - "inputs": { - "adv|use_file_names_as_ids": true, - "assembly_csv": { - "id": "1b325227d95fdc76", - "src": "hda" - }, - "assembly_plan_name": "BioBrickStandardAssembly", - "genbank_files": { - "id": "a363c57bce5ddac4", - "src": "hdca" - }, - "topology": "circular" - }, - "job": { - "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/4/8/f/dataset_48f246fb-df3d-4c65-a99e-cc314c9a2d20.dat,/tmp/tmps36anksu/files/5/0/c/dataset_50cb308d-4eb5-4d9d-ae07-011179d84b2e.dat,/tmp/tmps36anksu/files/1/3/b/dataset_13b514d1-710c-46ef-9b83-939acad72375.dat,/tmp/tmps36anksu/files/3/0/b/dataset_30bef7c3-fecb-40f7-b435-daf794d456c1.dat,/tmp/tmps36anksu/files/a/8/7/dataset_a87d7ba7-2092-45e2-9aff-813bb53a02a6.dat' --domesticated_seq '' --assembly_csv '/tmp/tmps36anksu/files/7/e/6/dataset_7e6259bf-8646-4691-b40d-d91bbe52d6c5.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmps36anksu/files/4/8/f/dataset_48f246fb-df3d-4c65-a99e-cc314c9a2d20.dat:BBa_E0040_GFP.gb,/tmp/tmps36anksu/files/5/0/c/dataset_50cb308d-4eb5-4d9d-ae07-011179d84b2e.dat:BBa_J23119_prom.gb,/tmp/tmps36anksu/files/1/3/b/dataset_13b514d1-710c-46ef-9b83-939acad72375.dat:BBa_J23119_prom_flawed.gb,/tmp/tmps36anksu/files/3/0/b/dataset_30bef7c3-fecb-40f7-b435-daf794d456c1.dat:BBa_J61048_term.gb,/tmp/tmps36anksu/files/a/8/7/dataset_a87d7ba7-2092-45e2-9aff-813bb53a02a6.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/35/outputs/dataset_664a6a95-4ce6-4f74-be51-728a9cbd55da.dat'", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-05-16T08:56:41.646034", + "create_time": "2025-05-16T12:37:15.245845", "dependencies": [ { "cacheable": false, @@ -805,7 +753,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", @@ -827,7 +775,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", @@ -849,7 +797,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", @@ -871,7 +819,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", @@ -893,7 +841,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", @@ -915,7 +863,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", @@ -937,7 +885,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", @@ -959,49 +907,49 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", - "version": "3.1.4" + "version": "3.1.5" } ], "exit_code": 0, - "external_id": "71459", + "external_id": "206517", "galaxy_version": "24.2", "handler": null, - "history_id": "a363c57bce5ddac4", - "id": "4d500d87322140a3", + "history_id": "4dd0eedec5562f6e", + "id": "920c0db56b0a806b", "inputs": { "assembly_csv": { - "id": "1b325227d95fdc76", + "id": "df13d5ca39cba7c4", "src": "hda", - "uuid": "7e6259bf-8646-4691-b40d-d91bbe52d6c5" + "uuid": "e971a6cf-b13e-4a65-a78d-aa22a0ea1fff" }, "genbank_files1": { - "id": "2d4530cd892a2a69", + "id": "caecbbc14917ac69", "src": "hda", - "uuid": "48f246fb-df3d-4c65-a99e-cc314c9a2d20" + "uuid": "4f0d4258-2f50-4a4e-9271-58e8c272856e" }, "genbank_files2": { - "id": "afd885e9dc2aeeee", + "id": "10cd084c8017547c", "src": "hda", - "uuid": "50cb308d-4eb5-4d9d-ae07-011179d84b2e" + "uuid": "27f67c7a-5e38-4103-a00b-a9d8234b6686" }, "genbank_files3": { - "id": "ae8033db013a49b9", + "id": "aa3451be0c94f76e", "src": "hda", - "uuid": "13b514d1-710c-46ef-9b83-939acad72375" + "uuid": "4e880afa-3f37-43a4-982e-36d750aab3d3" }, "genbank_files4": { - "id": "0661f11e9507b8a6", + "id": "a5f159065ae97d01", "src": "hda", - "uuid": "30bef7c3-fecb-40f7-b435-daf794d456c1" + "uuid": "3746bcc6-ee0c-4936-832f-ce29f808430d" }, "genbank_files5": { - "id": "fcc678ee7e8e9f81", + "id": "a001a939426dadd1", "src": "hda", - "uuid": "a87d7ba7-2092-45e2-9aff-813bb53a02a6" + "uuid": "788ebd7b-6247-4f96-a3d3-3c3306c210a0" } }, "job_messages": [], @@ -1010,67 +958,68 @@ "job_stderr": "", "job_stdout": "", "model_class": "Job", - "output_collections": {}, + "output_collections": { + "construct_gb": { + "id": "052d0d471d180256", + "src": "hdca" + } + }, "outputs": { "output_zip": { - "id": "4d500d87322140a3", + "id": "081ab14c99ce168b", "src": "hda", - "uuid": "664a6a95-4ce6-4f74-be51-728a9cbd55da" + "uuid": "5e0faa51-141c-49d1-ba84-ca8aba27508c" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", - "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "assembly_plan_name": "\"BASICAssembly\"", + "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, - "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", + "genbank_files": "{\"values\": [{\"id\": 7, \"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, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_parts_graph.pdf\nassambly_simulation/C3_final/C3_final.gb\nassambly_simulation/C3_final/C3_final_summary.csv\nassambly_simulation/C3_final/C3_final.pdf\nassambly_simulation/C3_final/provided_parts_records/C1_prom_barcode.gb\nassambly_simulation/C3_final/provided_parts_records/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_summary.csv\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_J61048_term.gb\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_E0040_GFP.gb\nassambly_simulation/all_construct_records/C1_prom_barcode.gb\nassambly_simulation/all_construct_records/C2_gfp_term.gb\nassambly_simulation/all_construct_records/C3_final.gb\nassambly_simulation/part_records/BBa_J61048_term.gb\nassambly_simulation/part_records/BBa_K611094_bar.gb\nassambly_simulation/part_records/BBa_E0040_GFP.gb\nassambly_simulation/part_records/BBa_J23119_prom.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_summary.csv\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_K611094_bar.gb\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_J23119_prom.gb\n", + "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.70it/s, now=None]\r \r", + "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%| | 0/3 [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, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C1_prom_barcode_E+S_restriction_connections_graph.pdf\nassambly_simulation/C3_final/C3_final_C2_gfp_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C3_final/C3_final_assembly_mix_parts_graph.pdf\nassambly_simulation/C3_final/C3_final.gb\nassambly_simulation/C3_final/C3_final_summary.csv\nassambly_simulation/C3_final/C3_final.pdf\nassambly_simulation/C3_final/provided_parts_records/C1_prom_barcode.gb\nassambly_simulation/C3_final/provided_parts_records/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_parts_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.gb\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_J61048_term_E+X_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_assembly_mix_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_BBa_E0040_GFP_E+S_restriction_connections_graph.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term.pdf\nassambly_simulation/C2_gfp_term/C2_gfp_term_summary.csv\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_J61048_term.gb\nassambly_simulation/C2_gfp_term/provided_parts_records/BBa_E0040_GFP.gb\nassambly_simulation/all_construct_records/C1_prom_barcode.gb\nassambly_simulation/all_construct_records/C2_gfp_term.gb\nassambly_simulation/all_construct_records/C3_final.gb\nassambly_simulation/part_records/BBa_J61048_term.gb\nassambly_simulation/part_records/BBa_K611094_bar.gb\nassambly_simulation/part_records/BBa_E0040_GFP.gb\nassambly_simulation/part_records/BBa_J23119_prom.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.gb\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_K611094_bar_E+S_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_summary.csv\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_assembly_mix_parts_graph.pdf\nassambly_simulation/C1_prom_barcode/C1_prom_barcode_BBa_J23119_prom_E+X_restriction_connections_graph.pdf\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_K611094_bar.gb\nassambly_simulation/C1_prom_barcode/provided_parts_records/BBa_J23119_prom.gb\n", - "update_time": "2025-05-16T08:56:55.140287", + "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 49.70it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "update_time": "2025-05-16T12:37:25.925491", "user_email": "planemo@galaxyproject.org", - "user_id": "1d1943aa60deb628" + "user_id": "a7025157dd5d3039" }, "status": "success", - "test_index": 4, - "time_seconds": 34.888214349746704, + "test_index": 3, + "time_seconds": 31.832648515701294, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, - "id": "cloning_simulation-4" + "id": "cloning_simulation-3" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "a727d841eabfe479", + "id": "6af8c0d3c72d39ba", "src": "hda" }, - "assembly_plan_name": "Type2sRestrictionAssembly", - "domesticated_input": { - "id": "8ab843ac4a5890da", - "src": "hdca" - }, + "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "6206f91299006d13", + "id": "5827a0347340e98b", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmps36anksu/files/2/b/3/dataset_2b34f95b-2776-40a7-ac0a-abdb3d2b151f.dat,/tmp/tmps36anksu/files/8/1/5/dataset_81535329-42d0-4e9d-a713-beb8033e2db9.dat,/tmp/tmps36anksu/files/d/b/b/dataset_dbbc8408-63b6-4265-8878-94942c7b2016.dat,/tmp/tmps36anksu/files/4/1/d/dataset_41d94b9c-f2f0-4253-88bb-896b26fdb7a0.dat,/tmp/tmps36anksu/files/4/8/a/dataset_48a630fc-ea4b-4c19-8b0b-fb78db4bff7d.dat,/tmp/tmps36anksu/files/4/5/9/dataset_459d85d8-4869-4d03-bd2a-d083e4ecf818.dat,/tmp/tmps36anksu/files/1/b/1/dataset_1b189627-18cd-4c7c-8d19-46371420574a.dat' --domesticated_seq '/tmp/tmps36anksu/files/6/a/2/dataset_6a2287bd-1281-4c99-89a6-e4af944c272a.dat,/tmp/tmps36anksu/files/2/c/9/dataset_2c942443-9fa9-48a9-bf35-2f8c2258967b.dat,/tmp/tmps36anksu/files/b/e/c/dataset_becfbff9-15f1-4830-b192-93e7892f371d.dat,/tmp/tmps36anksu/files/8/7/6/dataset_876d6160-fcd5-49e1-ae58-aa8d30c94e09.dat,/tmp/tmps36anksu/files/3/a/8/dataset_3a81169d-4569-4c6d-9417-a3c5924f8649.dat' --assembly_csv '/tmp/tmps36anksu/files/4/a/b/dataset_4abb21a9-cb77-4f0c-9a76-3c01fd662d2a.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmps36anksu/files/2/b/3/dataset_2b34f95b-2776-40a7-ac0a-abdb3d2b151f.dat:part_A.gb,/tmp/tmps36anksu/files/8/1/5/dataset_81535329-42d0-4e9d-a713-beb8033e2db9.dat:part_B.gb,/tmp/tmps36anksu/files/d/b/b/dataset_dbbc8408-63b6-4265-8878-94942c7b2016.dat:part_C.gb,/tmp/tmps36anksu/files/4/1/d/dataset_41d94b9c-f2f0-4253-88bb-896b26fdb7a0.dat:part_D.gb,/tmp/tmps36anksu/files/4/8/a/dataset_48a630fc-ea4b-4c19-8b0b-fb78db4bff7d.dat:part_E.gb,/tmp/tmps36anksu/files/4/5/9/dataset_459d85d8-4869-4d03-bd2a-d083e4ecf818.dat:part_F.gb,/tmp/tmps36anksu/files/1/b/1/dataset_1b189627-18cd-4c7c-8d19-46371420574a.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmps36anksu/files/6/a/2/dataset_6a2287bd-1281-4c99-89a6-e4af944c272a.dat:part_H.gb,/tmp/tmps36anksu/files/2/c/9/dataset_2c942443-9fa9-48a9-bf35-2f8c2258967b.dat:part_I.gb,/tmp/tmps36anksu/files/b/e/c/dataset_becfbff9-15f1-4830-b192-93e7892f371d.dat:part_J.gb,/tmp/tmps36anksu/files/8/7/6/dataset_876d6160-fcd5-49e1-ae58-aa8d30c94e09.dat:part_K.gb,/tmp/tmps36anksu/files/3/a/8/dataset_3a81169d-4569-4c6d-9417-a3c5924f8649.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmps36anksu/job_working_directory/000/49/outputs/dataset_891d2044-502b-4e4b-b394-575c9e42a36f.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/4/e/d/dataset_4ed60503-3b9f-4204-a8e9-0b96f76b1e49.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat:BBa_E0040_GFP.gb,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat:BBa_J23119_prom.gb,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat:BBa_J23119_prom_flawed.gb,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat:BBa_J61048_term.gb,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmph0r87skq/job_working_directory/000/35/outputs/dataset_5776ccd7-5dca-4f21-b288-9c15a0b9cdca.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-16T08:57:35.145295", + "create_time": "2025-05-16T12:37:47.708969", "dependencies": [ { "cacheable": false, @@ -1088,7 +1037,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "flametree", @@ -1110,7 +1059,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "biopython", @@ -1132,7 +1081,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "proglog", @@ -1154,7 +1103,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pandas", @@ -1176,7 +1125,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dnacauldron", @@ -1198,7 +1147,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "pdf-reports", @@ -1220,7 +1169,7 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "sequenticon", @@ -1242,84 +1191,49 @@ "versionless": false }, "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", "exact": true, "model_class": "MergedCondaDependency", "name": "dna_features_viewer", - "version": "3.1.4" + "version": "3.1.5" } ], "exit_code": 0, - "external_id": "72541", + "external_id": "207114", "galaxy_version": "24.2", "handler": null, - "history_id": "8ab843ac4a5890da", - "id": "9d82ca4e11899647", + "history_id": "d1cbd0905c1fc860", + "id": "081ab14c99ce168b", "inputs": { "assembly_csv": { - "id": "a727d841eabfe479", - "src": "hda", - "uuid": "4abb21a9-cb77-4f0c-9a76-3c01fd662d2a" - }, - "domesticated_input1": { - "id": "3437b137460a9bf9", - "src": "hda", - "uuid": "6a2287bd-1281-4c99-89a6-e4af944c272a" - }, - "domesticated_input2": { - "id": "4e00b6593169f669", + "id": "6af8c0d3c72d39ba", "src": "hda", - "uuid": "2c942443-9fa9-48a9-bf35-2f8c2258967b" - }, - "domesticated_input3": { - "id": "348e227de2cf9bbe", - "src": "hda", - "uuid": "becfbff9-15f1-4830-b192-93e7892f371d" - }, - "domesticated_input4": { - "id": "cb7d74ca0f50a91c", - "src": "hda", - "uuid": "876d6160-fcd5-49e1-ae58-aa8d30c94e09" - }, - "domesticated_input5": { - "id": "f0efc768d058218e", - "src": "hda", - "uuid": "3a81169d-4569-4c6d-9417-a3c5924f8649" + "uuid": "4ed60503-3b9f-4204-a8e9-0b96f76b1e49" }, "genbank_files1": { - "id": "4e56a0aaa45feaf7", + "id": "06bb6ed11a5684d2", "src": "hda", - "uuid": "2b34f95b-2776-40a7-ac0a-abdb3d2b151f" + "uuid": "773be428-2d30-4b95-9894-d3758634a3d0" }, "genbank_files2": { - "id": "cb872b8bb704ec40", + "id": "f34ce69b933b349e", "src": "hda", - "uuid": "81535329-42d0-4e9d-a713-beb8033e2db9" + "uuid": "bac673f5-074c-4810-9949-59d3b228d83c" }, "genbank_files3": { - "id": "90f63057cb36f606", + "id": "c295924a5ace6ae8", "src": "hda", - "uuid": "dbbc8408-63b6-4265-8878-94942c7b2016" + "uuid": "e5b8dfd0-6e81-47e4-b899-08976d0a1724" }, "genbank_files4": { - "id": "efde02d124a713a2", + "id": "f3a950b5ccc2e145", "src": "hda", - "uuid": "41d94b9c-f2f0-4253-88bb-896b26fdb7a0" + "uuid": "158cbebb-69fc-4333-b783-e9171b5324d6" }, "genbank_files5": { - "id": "81a37b9282573f69", - "src": "hda", - "uuid": "48a630fc-ea4b-4c19-8b0b-fb78db4bff7d" - }, - "genbank_files6": { - "id": "9989729bf7df579e", + "id": "486d488c3f12b41a", "src": "hda", - "uuid": "459d85d8-4869-4d03-bd2a-d083e4ecf818" - }, - "genbank_files7": { - "id": "bc2865f07ef20436", - "src": "hda", - "uuid": "1b189627-18cd-4c7c-8d19-46371420574a" + "uuid": "a5b6ae8b-1068-416f-b0ac-1c44e299cb87" } }, "job_messages": [], @@ -1328,37 +1242,400 @@ "job_stderr": "", "job_stdout": "", "model_class": "Job", - "output_collections": {}, + "output_collections": { + "construct_gb": { + "id": "26800a0030991202", + "src": "hdca" + } + }, "outputs": { + "__new_primary_file_construct_gb|C1_prom_barcode__": { + "id": "62952fe061c1d5d6", + "src": "hda", + "uuid": "fb185bc3-4c8e-4095-864e-edc42d8c87ab" + }, + "__new_primary_file_construct_gb|C2_gfp_term__": { + "id": "14c055702e438446", + "src": "hda", + "uuid": "cb6310a2-1237-4f80-9efa-f149cb896f4d" + }, + "__new_primary_file_construct_gb|C3_final__": { + "id": "e9ef3e2f0e439cf2", + "src": "hda", + "uuid": "13db93e9-4505-4542-845c-57029b5e9a89" + }, "output_zip": { - "id": "9d82ca4e11899647", + "id": "7f1cb49d27c5ee0d", "src": "hda", - "uuid": "891d2044-502b-4e4b-b394-575c9e42a36f" + "uuid": "5776ccd7-5dca-4f21-b288-9c15a0b9cdca" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", + "assembly_plan_name": "\"BioBrickStandardAssembly\"", + "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "domesticated_input": null, + "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", + "topology": "\"circular\"" + }, + "state": "ok", + "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/s, now=None]\r \r", + "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", + "tool_id": "cloning_simulation", + "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", + "update_time": "2025-05-16T12:38:00.688550", + "user_email": "planemo@galaxyproject.org", + "user_id": "a7025157dd5d3039" + }, + "status": "success", + "test_index": 4, + "time_seconds": 34.85270929336548, + "tool_id": "cloning_simulation", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "cloning_simulation-4" + }, + { + "data": { + "inputs": { + "adv|use_file_names_as_ids": true, + "assembly_csv": { + "id": "4e0765e9771b7fbe", + "src": "hda" + }, + "assembly_plan_name": "Type2sRestrictionAssembly", + "domesticated_input": { + "id": "9e9c740782c078df", + "src": "hdca" + }, + "genbank_files": { + "id": "d70a40a14f24deac", + "src": "hdca" + }, + "topology": "circular" + }, + "job": { + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat' --domesticated_seq '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.dat' --assembly_csv '/tmp/tmph0r87skq/files/c/6/5/dataset_c652bef1-f073-431c-9e5b-956a58e85d22.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat:part_A.gb,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat:part_B.gb,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat:part_C.gb,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat:part_D.gb,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat:part_E.gb,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat:part_F.gb,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat:part_H.gb,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat:part_I.gb,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat:part_J.gb,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat:part_K.gb,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmph0r87skq/job_working_directory/000/49/outputs/dataset_a88370aa-4d36-4867-b0d6-613cc59ed01a.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-16T12:38:41.107674", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "flametree", + "version": "0.1.11" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "biopython", + "version": "1.85" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "proglog", + "version": "0.1.10" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": 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+ "uuid": "9e21455c-b124-4c01-8524-949ff16b570e" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": { + "construct_gb": { + "id": "c02153e44a10e06a", + "src": "hdca" + } + }, + "outputs": { + "__new_primary_file_construct_gb|construct_1__": { + "id": "a3a16f375ef01612", + "src": "hda", + "uuid": "760d3bcc-0498-4f4a-9420-511468a0b0b3" + }, + "__new_primary_file_construct_gb|construct_2__": { + "id": "99e6c6e9665a5a56", + "src": "hda", + "uuid": "9836288d-70fb-464e-b565-90dc8f966379" + }, + "__new_primary_file_construct_gb|construct_3__": { + "id": "2d10fdf290562ab3", + "src": "hda", + "uuid": "cf0e5bca-9446-4574-b885-ab1636310493" + }, + "__new_primary_file_construct_gb|construct_4__": { + "id": "071f312ace6db7aa", + "src": "hda", + "uuid": "9e552d2e-e5f3-4163-b4b4-6351ec76f0d3" + }, + "output_zip": { + "id": "72a012487a44f1a3", + "src": "hda", + "uuid": 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[00:01<00:00, 2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", - "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", + "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", - "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nFiles in the zip archive:\nassambly_simulation/assambly_all_required_parts.txt\nassambly_simulation/assambly_constructs_level_2.csv\nassambly_simulation/assambly_simulation_stats.csv\nassambly_simulation/assambly_constructs_level_1.csv\nassambly_simulation/Report.pdf\nassambly_simulation/assembly_plan_graph.pdf\nassambly_simulation/assambly_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_3/construct_3_summary.csv\nassambly_simulation/construct_3/construct_3_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_3/construct_3.gb\nassambly_simulation/construct_3/construct_3.pdf\nassambly_simulation/construct_3/provided_parts_records/part_L.gb\nassambly_simulation/construct_3/provided_parts_records/part_K.gb\nassambly_simulation/construct_3/provided_parts_records/part_J.gb\nassambly_simulation/construct_3/provided_parts_records/construct_1.gb\nassambly_simulation/all_construct_records/construct_2.gb\nassambly_simulation/all_construct_records/construct_3.gb\nassambly_simulation/all_construct_records/construct_4.gb\nassambly_simulation/all_construct_records/construct_1.gb\nassambly_simulation/construct_1/construct_1_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_1/construct_1_summary.csv\nassambly_simulation/construct_1/construct_1_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_1/construct_1.pdf\nassambly_simulation/construct_1/construct_1.gb\nassambly_simulation/construct_1/provided_parts_records/part_F.gb\nassambly_simulation/construct_1/provided_parts_records/part_B.gb\nassambly_simulation/construct_1/provided_parts_records/part_D.gb\nassambly_simulation/construct_1/provided_parts_records/part_A.gb\nassambly_simulation/construct_1/provided_parts_records/part_C.gb\nassambly_simulation/construct_1/provided_parts_records/part_E.gb\nassambly_simulation/part_records/part_L.gb\nassambly_simulation/part_records/part_F.gb\nassambly_simulation/part_records/part_B.gb\nassambly_simulation/part_records/part_K.gb\nassambly_simulation/part_records/part_D.gb\nassambly_simulation/part_records/part_A.gb\nassambly_simulation/part_records/part_C.gb\nassambly_simulation/part_records/part_G.gb\nassambly_simulation/part_records/part_I.gb\nassambly_simulation/part_records/part_E.gb\nassambly_simulation/part_records/part_J.gb\nassambly_simulation/part_records/part_H.gb\nassambly_simulation/construct_2/construct_2_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_2/construct_2.pdf\nassambly_simulation/construct_2/construct_2.gb\nassambly_simulation/construct_2/construct_2_summary.csv\nassambly_simulation/construct_2/construct_2_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_2/provided_parts_records/part_F.gb\nassambly_simulation/construct_2/provided_parts_records/part_A.gb\nassambly_simulation/construct_2/provided_parts_records/part_G.gb\nassambly_simulation/construct_2/provided_parts_records/part_I.gb\nassambly_simulation/construct_2/provided_parts_records/part_H.gb\nassambly_simulation/construct_4/construct_4_type2s_mix_parts_graph.pdf\nassambly_simulation/construct_4/construct_4.pdf\nassambly_simulation/construct_4/construct_4.gb\nassambly_simulation/construct_4/construct_4_summary.csv\nassambly_simulation/construct_4/construct_4_type2s_mix_connections_graph.pdf\nassambly_simulation/construct_4/provided_parts_records/part_L.gb\nassambly_simulation/construct_4/provided_parts_records/part_K.gb\nassambly_simulation/construct_4/provided_parts_records/construct_2.gb\nassambly_simulation/construct_4/provided_parts_records/part_J.gb\n", - "update_time": "2025-05-16T08:57:47.925883", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", + "update_time": "2025-05-16T12:38:53.803402", "user_email": "planemo@galaxyproject.org", - "user_id": "1d1943aa60deb628" + "user_id": "a7025157dd5d3039" }, "status": "success", "test_index": 5, - "time_seconds": 52.77062439918518, + "time_seconds": 52.96998858451843, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" },