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comparison output.json @ 3:044d36066cb3 draft

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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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2:3171db614963 3:044d36066cb3
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "adv|use_file_names_as_ids": true, 12 "adv|use_file_names_as_ids": true,
13 "assembly_csv": { 13 "assembly_csv": {
14 "id": "a2e8f3fd1611e7f5", 14 "id": "c02153e44a10e06a",
15 "src": "hda" 15 "src": "hda"
16 }, 16 },
17 "assembly_plan_name": "Type2sRestrictionAssembly", 17 "assembly_plan_name": "Type2sRestrictionAssembly",
18 "genbank_files": { 18 "genbank_files": {
19 "id": "1d1943aa60deb628", 19 "id": "a7025157dd5d3039",
20 "src": "hdca" 20 "src": "hdca"
21 }, 21 },
22 "topology": "circular" 22 "topology": "circular"
23 }, 23 },
24 "job": { 24 "job": {
25 "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'", 25 "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'",
26 "command_version": "", 26 "command_version": "",
27 "copied_from_job_id": null, 27 "copied_from_job_id": null,
28 "create_time": "2025-05-16T08:54:45.629427", 28 "create_time": "2025-05-16T12:35:55.635805",
29 "dependencies": [], 29 "dependencies": [],
30 "exit_code": 0, 30 "exit_code": 0,
31 "external_id": "69472", 31 "external_id": "205109",
32 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
33 "handler": null, 33 "handler": null,
34 "history_id": "1d1943aa60deb628", 34 "history_id": "a7025157dd5d3039",
35 "id": "306d449b91ecb0a3", 35 "id": "d49d8be9932a8ee0",
36 "inputs": { 36 "inputs": {
37 "assembly_csv": { 37 "assembly_csv": {
38 "id": "a2e8f3fd1611e7f5", 38 "id": "c02153e44a10e06a",
39 "src": "hda", 39 "src": "hda",
40 "uuid": "420c4b07-ea17-4e63-9f48-4cc364e28432" 40 "uuid": "a522972a-c994-4ec0-a130-e3e1e101d126"
41 }, 41 },
42 "genbank_files1": { 42 "genbank_files1": {
43 "id": "1d1943aa60deb628", 43 "id": "a7025157dd5d3039",
44 "src": "hda", 44 "src": "hda",
45 "uuid": "6a407f29-14a2-4358-8781-97a5a60006bf" 45 "uuid": "eb40ee5e-5155-4303-9230-94926c63daaf"
46 }, 46 },
47 "genbank_files10": { 47 "genbank_files10": {
48 "id": "b55875807068e59e", 48 "id": "26800a0030991202",
49 "src": "hda", 49 "src": "hda",
50 "uuid": "23c06fae-96cc-4ff8-9e23-111139ce1a92" 50 "uuid": "184d9904-3705-424e-b3f7-e5b7b773880f"
51 }, 51 },
52 "genbank_files11": { 52 "genbank_files11": {
53 "id": "4b64a67f616af776", 53 "id": "9e9c740782c078df",
54 "src": "hda", 54 "src": "hda",
55 "uuid": "d29c16a7-2470-418e-a8f1-1da7c5372dde" 55 "uuid": "4a10d392-6ebc-413c-bd71-db425aa1aa0a"
56 }, 56 },
57 "genbank_files12": { 57 "genbank_files12": {
58 "id": "1fda217ac9617c88", 58 "id": "d70a40a14f24deac",
59 "src": "hda", 59 "src": "hda",
60 "uuid": "290bfdf4-f595-42f1-a2f0-0f9a9d8e71df" 60 "uuid": "835878c6-84f1-465c-b34e-d177885e567d"
61 }, 61 },
62 "genbank_files2": { 62 "genbank_files2": {
63 "id": "13a3899f03fff34a", 63 "id": "ce87194f2a532da8",
64 "src": "hda", 64 "src": "hda",
65 "uuid": "9c05120b-2a93-4298-a718-2db482dec9e0" 65 "uuid": "4a9a1335-c528-438d-b80a-62b9608dbade"
66 }, 66 },
67 "genbank_files3": { 67 "genbank_files3": {
68 "id": "6872e1ad22eb2e5d", 68 "id": "e52e8d0a017d5bd2",
69 "src": "hda", 69 "src": "hda",
70 "uuid": "e9dd6c4a-5d1c-48d6-b072-bb67929590f5" 70 "uuid": "7caa4f6a-a734-461f-ac38-c95442632c5a"
71 }, 71 },
72 "genbank_files4": { 72 "genbank_files4": {
73 "id": "248d7f69d2402068", 73 "id": "4dd0eedec5562f6e",
74 "src": "hda", 74 "src": "hda",
75 "uuid": "c2a67b9c-bd0d-483b-b229-1f396bc8c275" 75 "uuid": "93127db8-2409-4544-93e5-6243a6d253ef"
76 }, 76 },
77 "genbank_files5": { 77 "genbank_files5": {
78 "id": "a363c57bce5ddac4", 78 "id": "d1cbd0905c1fc860",
79 "src": "hda", 79 "src": "hda",
80 "uuid": "53dc6b3e-3d2b-4fb7-b279-8b7204ae8d00" 80 "uuid": "e292919e-0a9a-403a-aa6b-30aa552881bd"
81 }, 81 },
82 "genbank_files6": { 82 "genbank_files6": {
83 "id": "8ab843ac4a5890da", 83 "id": "0494b81690cb2f5c",
84 "src": "hda", 84 "src": "hda",
85 "uuid": "40fa89b4-5e49-467e-aa6a-d4b8c9b8a8b0" 85 "uuid": "4a7c1e6b-f470-414e-b533-7390f74a64fc"
86 }, 86 },
87 "genbank_files7": { 87 "genbank_files7": {
88 "id": "6206f91299006d13", 88 "id": "edce0bc0654ca8cc",
89 "src": "hda", 89 "src": "hda",
90 "uuid": "14b815cb-038e-4836-bb4e-3f049395271c" 90 "uuid": "7f3df904-0bc5-456a-8679-cc58d06e214e"
91 }, 91 },
92 "genbank_files8": { 92 "genbank_files8": {
93 "id": "278f145ab0478700", 93 "id": "052d0d471d180256",
94 "src": "hda", 94 "src": "hda",
95 "uuid": "32719970-8009-4818-a623-ba980af84d70" 95 "uuid": "a605738c-9b6d-44c6-891e-01cb729ea4dc"
96 }, 96 },
97 "genbank_files9": { 97 "genbank_files9": {
98 "id": "84aedadb70ef205b", 98 "id": "5827a0347340e98b",
99 "src": "hda", 99 "src": "hda",
100 "uuid": "68e30a2d-a44d-40e6-a619-efa1e8cd6e4b" 100 "uuid": "10c35405-af25-41d3-9dbd-a411b4b65b98"
101 } 101 }
102 }, 102 },
103 "job_messages": [], 103 "job_messages": [],
104 "job_metrics": [], 104 "job_metrics": [],
105 "job_runner_name": null, 105 "job_runner_name": null,
106 "job_stderr": "", 106 "job_stderr": "",
107 "job_stdout": "", 107 "job_stdout": "",
108 "model_class": "Job", 108 "model_class": "Job",
109 "output_collections": {}, 109 "output_collections": {
110 "construct_gb": {
111 "id": "ce87194f2a532da8",
112 "src": "hdca"
113 }
114 },
110 "outputs": { 115 "outputs": {
116 "__new_primary_file_construct_gb|construct_1__": {
117 "id": "68bcb17f47b988de",
118 "src": "hda",
119 "uuid": "2c9a5458-38f0-4591-bb2d-452aac86ce0b"
120 },
121 "__new_primary_file_construct_gb|construct_2__": {
122 "id": "7cb8b41737d3d7aa",
123 "src": "hda",
124 "uuid": "026f0937-350b-4ae7-96da-1e685237a8c8"
125 },
126 "__new_primary_file_construct_gb|construct_3__": {
127 "id": "e558db6e0f20f34c",
128 "src": "hda",
129 "uuid": "df750e5d-b2f4-43f1-bf95-aa0d980bb98a"
130 },
131 "__new_primary_file_construct_gb|construct_4__": {
132 "id": "87544afc708050c8",
133 "src": "hda",
134 "uuid": "0ba9a694-1b4e-4ff4-b6f2-87503d04cd66"
135 },
111 "output_zip": { 136 "output_zip": {
112 "id": "306d449b91ecb0a3", 137 "id": "d49d8be9932a8ee0",
113 "src": "hda", 138 "src": "hda",
114 "uuid": "19827d46-96d8-48c8-b434-17f9e4732aec" 139 "uuid": "109d2ac1-716e-4c47-a2b9-25e9d68cd9b7"
115 } 140 }
116 }, 141 },
117 "params": { 142 "params": {
118 "__input_ext": "\"input\"", 143 "__input_ext": "\"input\"",
119 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 144 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
120 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 145 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
121 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 146 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
122 "dbkey": "\"?\"", 147 "dbkey": "\"?\"",
123 "domesticated_input": null, 148 "domesticated_input": null,
124 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", 149 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
125 "topology": "\"circular\"" 150 "topology": "\"circular\""
126 }, 151 },
127 "state": "ok", 152 "state": "ok",
128 "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", 153 "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",
129 "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", 154 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
130 "tool_id": "cloning_simulation", 155 "tool_id": "cloning_simulation",
131 "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", 156 "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",
132 "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", 157 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
133 "update_time": "2025-05-16T08:54:59.050276", 158 "update_time": "2025-05-16T12:36:09.065234",
134 "user_email": "planemo@galaxyproject.org", 159 "user_email": "planemo@galaxyproject.org",
135 "user_id": "1d1943aa60deb628" 160 "user_id": "a7025157dd5d3039"
136 }, 161 },
137 "status": "success", 162 "status": "success",
138 "test_index": 0, 163 "test_index": 0,
139 "time_seconds": 53.80709099769592, 164 "time_seconds": 54.82133865356445,
140 "tool_id": "cloning_simulation", 165 "tool_id": "cloning_simulation",
141 "tool_version": "0.1.0+galaxy0" 166 "tool_version": "0.1.0+galaxy0"
142 }, 167 },
143 "has_data": true, 168 "has_data": true,
144 "id": "cloning_simulation-0" 169 "id": "cloning_simulation-0"
146 { 171 {
147 "data": { 172 "data": {
148 "inputs": { 173 "inputs": {
149 "adv|use_file_names_as_ids": true, 174 "adv|use_file_names_as_ids": true,
150 "assembly_csv": { 175 "assembly_csv": {
151 "id": "343611dad2e145e6", 176 "id": "13b114ac662002c6",
152 "src": "hda" 177 "src": "hda"
153 }, 178 },
154 "assembly_plan_name": "GibsonAssembly", 179 "assembly_plan_name": "GibsonAssembly",
155 "genbank_files": { 180 "genbank_files": {
156 "id": "13a3899f03fff34a", 181 "id": "e52e8d0a017d5bd2",
157 "src": "hdca" 182 "src": "hdca"
158 }, 183 },
159 "topology": "circular" 184 "topology": "circular"
160 }, 185 },
161 "job": { 186 "job": {
162 "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'", 187 "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'",
163 "command_version": "", 188 "command_version": "",
164 "copied_from_job_id": null, 189 "copied_from_job_id": null,
165 "create_time": "2025-05-16T08:55:10.522461", 190 "create_time": "2025-05-16T12:36:19.661290",
166 "dependencies": [ 191 "dependencies": [
167 { 192 {
168 "cacheable": false, 193 "cacheable": false,
169 "dependency_resolver": { 194 "dependency_resolver": {
170 "auto_init": true, 195 "auto_init": true,
178 "resolves_simple_dependencies": true, 203 "resolves_simple_dependencies": true,
179 "use_local": false, 204 "use_local": false,
180 "versionless": false 205 "versionless": false
181 }, 206 },
182 "dependency_type": "conda", 207 "dependency_type": "conda",
183 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 208 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
184 "exact": true, 209 "exact": true,
185 "model_class": "MergedCondaDependency", 210 "model_class": "MergedCondaDependency",
186 "name": "flametree", 211 "name": "flametree",
187 "version": "0.1.11" 212 "version": "0.1.11"
188 }, 213 },
200 "resolves_simple_dependencies": true, 225 "resolves_simple_dependencies": true,
201 "use_local": false, 226 "use_local": false,
202 "versionless": false 227 "versionless": false
203 }, 228 },
204 "dependency_type": "conda", 229 "dependency_type": "conda",
205 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 230 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
206 "exact": true, 231 "exact": true,
207 "model_class": "MergedCondaDependency", 232 "model_class": "MergedCondaDependency",
208 "name": "biopython", 233 "name": "biopython",
209 "version": "1.85" 234 "version": "1.85"
210 }, 235 },
222 "resolves_simple_dependencies": true, 247 "resolves_simple_dependencies": true,
223 "use_local": false, 248 "use_local": false,
224 "versionless": false 249 "versionless": false
225 }, 250 },
226 "dependency_type": "conda", 251 "dependency_type": "conda",
227 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 252 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
228 "exact": true, 253 "exact": true,
229 "model_class": "MergedCondaDependency", 254 "model_class": "MergedCondaDependency",
230 "name": "proglog", 255 "name": "proglog",
231 "version": "0.1.10" 256 "version": "0.1.10"
232 }, 257 },
244 "resolves_simple_dependencies": true, 269 "resolves_simple_dependencies": true,
245 "use_local": false, 270 "use_local": false,
246 "versionless": false 271 "versionless": false
247 }, 272 },
248 "dependency_type": "conda", 273 "dependency_type": "conda",
249 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 274 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
250 "exact": true, 275 "exact": true,
251 "model_class": "MergedCondaDependency", 276 "model_class": "MergedCondaDependency",
252 "name": "pandas", 277 "name": "pandas",
253 "version": "2.2.3" 278 "version": "2.2.3"
254 }, 279 },
266 "resolves_simple_dependencies": true, 291 "resolves_simple_dependencies": true,
267 "use_local": false, 292 "use_local": false,
268 "versionless": false 293 "versionless": false
269 }, 294 },
270 "dependency_type": "conda", 295 "dependency_type": "conda",
271 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 296 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
272 "exact": true, 297 "exact": true,
273 "model_class": "MergedCondaDependency", 298 "model_class": "MergedCondaDependency",
274 "name": "dnacauldron", 299 "name": "dnacauldron",
275 "version": "2.0.12" 300 "version": "2.0.12"
276 }, 301 },
288 "resolves_simple_dependencies": true, 313 "resolves_simple_dependencies": true,
289 "use_local": false, 314 "use_local": false,
290 "versionless": false 315 "versionless": false
291 }, 316 },
292 "dependency_type": "conda", 317 "dependency_type": "conda",
293 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 318 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
294 "exact": true, 319 "exact": true,
295 "model_class": "MergedCondaDependency", 320 "model_class": "MergedCondaDependency",
296 "name": "pdf-reports", 321 "name": "pdf-reports",
297 "version": "0.3.9" 322 "version": "0.3.9"
298 }, 323 },
310 "resolves_simple_dependencies": true, 335 "resolves_simple_dependencies": true,
311 "use_local": false, 336 "use_local": false,
312 "versionless": false 337 "versionless": false
313 }, 338 },
314 "dependency_type": "conda", 339 "dependency_type": "conda",
315 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 340 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
316 "exact": true, 341 "exact": true,
317 "model_class": "MergedCondaDependency", 342 "model_class": "MergedCondaDependency",
318 "name": "sequenticon", 343 "name": "sequenticon",
319 "version": "0.1.8" 344 "version": "0.1.8"
320 }, 345 },
332 "resolves_simple_dependencies": true, 357 "resolves_simple_dependencies": true,
333 "use_local": false, 358 "use_local": false,
334 "versionless": false 359 "versionless": false
335 }, 360 },
336 "dependency_type": "conda", 361 "dependency_type": "conda",
337 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 362 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
338 "exact": true, 363 "exact": true,
339 "model_class": "MergedCondaDependency", 364 "model_class": "MergedCondaDependency",
340 "name": "dna_features_viewer", 365 "name": "dna_features_viewer",
341 "version": "3.1.4" 366 "version": "3.1.5"
342 } 367 }
343 ], 368 ],
344 "exit_code": 0, 369 "exit_code": 0,
345 "external_id": "69816", 370 "external_id": "205459",
346 "galaxy_version": "24.2", 371 "galaxy_version": "24.2",
347 "handler": null, 372 "handler": null,
348 "history_id": "13a3899f03fff34a", 373 "history_id": "ce87194f2a532da8",
349 "id": "6fff2cd3fd6e4947", 374 "id": "e558db6e0f20f34c",
350 "inputs": { 375 "inputs": {
351 "assembly_csv": { 376 "assembly_csv": {
352 "id": "343611dad2e145e6", 377 "id": "13b114ac662002c6",
353 "src": "hda", 378 "src": "hda",
354 "uuid": "7a09a16a-a7f7-44ce-8e1d-5f6baf385c44" 379 "uuid": "579b13e6-f14d-401c-88ee-b25ed3bf42dc"
355 }, 380 },
356 "genbank_files1": { 381 "genbank_files1": {
357 "id": "03c59a54410e4ccf", 382 "id": "16385471cc722641",
358 "src": "hda", 383 "src": "hda",
359 "uuid": "5c2150b5-537a-4971-98ef-959bb4141fac" 384 "uuid": "f2e8406c-fdb7-4b30-aa74-202b93292a26"
360 } 385 }
361 }, 386 },
362 "job_messages": [], 387 "job_messages": [],
363 "job_metrics": [], 388 "job_metrics": [],
364 "job_runner_name": null, 389 "job_runner_name": null,
365 "job_stderr": "", 390 "job_stderr": "",
366 "job_stdout": "", 391 "job_stdout": "",
367 "model_class": "Job", 392 "model_class": "Job",
368 "output_collections": {}, 393 "output_collections": {
394 "construct_gb": {
395 "id": "4dd0eedec5562f6e",
396 "src": "hdca"
397 }
398 },
369 "outputs": { 399 "outputs": {
400 "__new_primary_file_construct_gb|construct_1__": {
401 "id": "eb4747fb10762624",
402 "src": "hda",
403 "uuid": "8b9f07c0-2a2f-49db-b0b9-e3b27b5d2102"
404 },
405 "__new_primary_file_construct_gb|construct_2__": {
406 "id": "fa2c1cd7e40ca607",
407 "src": "hda",
408 "uuid": "694f0f93-1c26-4a8b-91ed-bcb7fe4b3784"
409 },
410 "__new_primary_file_construct_gb|construct_3__": {
411 "id": "2c9180ba70391455",
412 "src": "hda",
413 "uuid": "e57dc6e8-10e6-4527-a375-9ed583735c59"
414 },
370 "output_zip": { 415 "output_zip": {
371 "id": "6fff2cd3fd6e4947", 416 "id": "cf8958f7b0d14fa5",
372 "src": "hda", 417 "src": "hda",
373 "uuid": "4c70b3f9-9fb4-4e1c-942c-47fd78a5a348" 418 "uuid": "36e0457f-1da8-456a-86c9-20ea242688bc"
374 } 419 }
375 }, 420 },
376 "params": { 421 "params": {
377 "__input_ext": "\"input\"", 422 "__input_ext": "\"input\"",
378 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 423 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
379 "assembly_plan_name": "\"GibsonAssembly\"", 424 "assembly_plan_name": "\"GibsonAssembly\"",
380 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 425 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
381 "dbkey": "\"?\"", 426 "dbkey": "\"?\"",
382 "domesticated_input": null, 427 "domesticated_input": null,
383 "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", 428 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
384 "topology": "\"circular\"" 429 "topology": "\"circular\""
385 }, 430 },
386 "state": "ok", 431 "state": "ok",
387 "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", 432 "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",
388 "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", 433 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
389 "tool_id": "cloning_simulation", 434 "tool_id": "cloning_simulation",
390 "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", 435 "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",
391 "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", 436 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
392 "update_time": "2025-05-16T08:55:23.301357", 437 "update_time": "2025-05-16T12:36:31.612352",
393 "user_email": "planemo@galaxyproject.org", 438 "user_email": "planemo@galaxyproject.org",
394 "user_id": "1d1943aa60deb628" 439 "user_id": "a7025157dd5d3039"
395 }, 440 },
396 "status": "success", 441 "status": "success",
397 "test_index": 1, 442 "test_index": 1,
398 "time_seconds": 24.055506706237793, 443 "time_seconds": 22.601666688919067,
399 "tool_id": "cloning_simulation", 444 "tool_id": "cloning_simulation",
400 "tool_version": "0.1.0+galaxy0" 445 "tool_version": "0.1.0+galaxy0"
401 }, 446 },
402 "has_data": true, 447 "has_data": true,
403 "id": "cloning_simulation-1" 448 "id": "cloning_simulation-1"
405 { 450 {
406 "data": { 451 "data": {
407 "inputs": { 452 "inputs": {
408 "adv|use_file_names_as_ids": true, 453 "adv|use_file_names_as_ids": true,
409 "assembly_csv": { 454 "assembly_csv": {
410 "id": "eae50b1e0ba0bca8", 455 "id": "84906eb14284db27",
411 "src": "hda" 456 "src": "hda"
412 }, 457 },
413 "assembly_plan_name": "LigaseCyclingReactionAssembly", 458 "assembly_plan_name": "LigaseCyclingReactionAssembly",
414 "genbank_files": { 459 "genbank_files": {
415 "id": "6872e1ad22eb2e5d", 460 "id": "d1cbd0905c1fc860",
416 "src": "hdca" 461 "src": "hdca"
417 }, 462 },
418 "topology": "circular" 463 "topology": "circular"
419 }, 464 },
420 "job": { 465 "job": {
421 "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'", 466 "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'",
422 "command_version": "", 467 "command_version": "",
423 "copied_from_job_id": null, 468 "copied_from_job_id": null,
424 "create_time": "2025-05-16T08:55:35.420052", 469 "create_time": "2025-05-16T12:36:42.888728",
425 "dependencies": [ 470 "dependencies": [
426 { 471 {
427 "cacheable": false, 472 "cacheable": false,
428 "dependency_resolver": { 473 "dependency_resolver": {
429 "auto_init": true, 474 "auto_init": true,
437 "resolves_simple_dependencies": true, 482 "resolves_simple_dependencies": true,
438 "use_local": false, 483 "use_local": false,
439 "versionless": false 484 "versionless": false
440 }, 485 },
441 "dependency_type": "conda", 486 "dependency_type": "conda",
442 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 487 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
443 "exact": true, 488 "exact": true,
444 "model_class": "MergedCondaDependency", 489 "model_class": "MergedCondaDependency",
445 "name": "flametree", 490 "name": "flametree",
446 "version": "0.1.11" 491 "version": "0.1.11"
447 }, 492 },
459 "resolves_simple_dependencies": true, 504 "resolves_simple_dependencies": true,
460 "use_local": false, 505 "use_local": false,
461 "versionless": false 506 "versionless": false
462 }, 507 },
463 "dependency_type": "conda", 508 "dependency_type": "conda",
464 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 509 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
465 "exact": true, 510 "exact": true,
466 "model_class": "MergedCondaDependency", 511 "model_class": "MergedCondaDependency",
467 "name": "biopython", 512 "name": "biopython",
468 "version": "1.85" 513 "version": "1.85"
469 }, 514 },
481 "resolves_simple_dependencies": true, 526 "resolves_simple_dependencies": true,
482 "use_local": false, 527 "use_local": false,
483 "versionless": false 528 "versionless": false
484 }, 529 },
485 "dependency_type": "conda", 530 "dependency_type": "conda",
486 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 531 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
487 "exact": true, 532 "exact": true,
488 "model_class": "MergedCondaDependency", 533 "model_class": "MergedCondaDependency",
489 "name": "proglog", 534 "name": "proglog",
490 "version": "0.1.10" 535 "version": "0.1.10"
491 }, 536 },
503 "resolves_simple_dependencies": true, 548 "resolves_simple_dependencies": true,
504 "use_local": false, 549 "use_local": false,
505 "versionless": false 550 "versionless": false
506 }, 551 },
507 "dependency_type": "conda", 552 "dependency_type": "conda",
508 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 553 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
509 "exact": true, 554 "exact": true,
510 "model_class": "MergedCondaDependency", 555 "model_class": "MergedCondaDependency",
511 "name": "pandas", 556 "name": "pandas",
512 "version": "2.2.3" 557 "version": "2.2.3"
513 }, 558 },
525 "resolves_simple_dependencies": true, 570 "resolves_simple_dependencies": true,
526 "use_local": false, 571 "use_local": false,
527 "versionless": false 572 "versionless": false
528 }, 573 },
529 "dependency_type": "conda", 574 "dependency_type": "conda",
530 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 575 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
531 "exact": true, 576 "exact": true,
532 "model_class": "MergedCondaDependency", 577 "model_class": "MergedCondaDependency",
533 "name": "dnacauldron", 578 "name": "dnacauldron",
534 "version": "2.0.12" 579 "version": "2.0.12"
535 }, 580 },
547 "resolves_simple_dependencies": true, 592 "resolves_simple_dependencies": true,
548 "use_local": false, 593 "use_local": false,
549 "versionless": false 594 "versionless": false
550 }, 595 },
551 "dependency_type": "conda", 596 "dependency_type": "conda",
552 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 597 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
553 "exact": true, 598 "exact": true,
554 "model_class": "MergedCondaDependency", 599 "model_class": "MergedCondaDependency",
555 "name": "pdf-reports", 600 "name": "pdf-reports",
556 "version": "0.3.9" 601 "version": "0.3.9"
557 }, 602 },
569 "resolves_simple_dependencies": true, 614 "resolves_simple_dependencies": true,
570 "use_local": false, 615 "use_local": false,
571 "versionless": false 616 "versionless": false
572 }, 617 },
573 "dependency_type": "conda", 618 "dependency_type": "conda",
574 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 619 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
575 "exact": true, 620 "exact": true,
576 "model_class": "MergedCondaDependency", 621 "model_class": "MergedCondaDependency",
577 "name": "sequenticon", 622 "name": "sequenticon",
578 "version": "0.1.8" 623 "version": "0.1.8"
579 }, 624 },
591 "resolves_simple_dependencies": true, 636 "resolves_simple_dependencies": true,
592 "use_local": false, 637 "use_local": false,
593 "versionless": false 638 "versionless": false
594 }, 639 },
595 "dependency_type": "conda", 640 "dependency_type": "conda",
596 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 641 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
597 "exact": true, 642 "exact": true,
598 "model_class": "MergedCondaDependency", 643 "model_class": "MergedCondaDependency",
599 "name": "dna_features_viewer", 644 "name": "dna_features_viewer",
600 "version": "3.1.4" 645 "version": "3.1.5"
601 } 646 }
602 ], 647 ],
603 "exit_code": 0, 648 "exit_code": 0,
604 "external_id": "70205", 649 "external_id": "205894",
605 "galaxy_version": "24.2", 650 "galaxy_version": "24.2",
606 "handler": null, 651 "handler": null,
607 "history_id": "6872e1ad22eb2e5d", 652 "history_id": "e52e8d0a017d5bd2",
608 "id": "8205956dbdec438f", 653 "id": "cf8958f7b0d14fa5",
609 "inputs": { 654 "inputs": {
610 "assembly_csv": { 655 "assembly_csv": {
611 "id": "eae50b1e0ba0bca8", 656 "id": "84906eb14284db27",
612 "src": "hda", 657 "src": "hda",
613 "uuid": "5af89b00-757d-4606-b6c8-d00d3f0ca39e" 658 "uuid": "20eb88b1-0fc5-476b-a409-da7f598780b6"
614 }, 659 },
615 "genbank_files1": { 660 "genbank_files1": {
616 "id": "e685210c6961cf21", 661 "id": "1fdafe0e70c0e721",
617 "src": "hda", 662 "src": "hda",
618 "uuid": "aa035ce9-b3ee-4c4d-a5c1-e2451c4297c2" 663 "uuid": "15741680-9963-4b3d-979e-792be37256f2"
619 }, 664 },
620 "genbank_files2": { 665 "genbank_files2": {
621 "id": "fb0119a6d133c713", 666 "id": "044728be18fd1186",
622 "src": "hda", 667 "src": "hda",
623 "uuid": "4bb2bf6a-b351-4a80-ab47-d4d56aefa38c" 668 "uuid": "d3de76b3-3793-46fa-990e-970e1bcb2a72"
624 } 669 }
625 }, 670 },
626 "job_messages": [], 671 "job_messages": [],
627 "job_metrics": [], 672 "job_metrics": [],
628 "job_runner_name": null, 673 "job_runner_name": null,
629 "job_stderr": "", 674 "job_stderr": "",
630 "job_stdout": "", 675 "job_stdout": "",
631 "model_class": "Job", 676 "model_class": "Job",
632 "output_collections": {}, 677 "output_collections": {
678 "construct_gb": {
679 "id": "0494b81690cb2f5c",
680 "src": "hdca"
681 }
682 },
633 "outputs": { 683 "outputs": {
634 "output_zip": { 684 "output_zip": {
635 "id": "8205956dbdec438f", 685 "id": "920c0db56b0a806b",
636 "src": "hda", 686 "src": "hda",
637 "uuid": "bd5c88b9-1efd-4507-b875-13dfebff9d6a" 687 "uuid": "0ffdda24-b80f-4db5-8c10-1467d34eb3a8"
638 } 688 }
639 }, 689 },
640 "params": { 690 "params": {
641 "__input_ext": "\"input\"", 691 "__input_ext": "\"input\"",
642 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 692 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
643 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", 693 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
644 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 694 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
645 "dbkey": "\"?\"", 695 "dbkey": "\"?\"",
646 "domesticated_input": null, 696 "domesticated_input": null,
647 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", 697 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
648 "topology": "\"circular\"" 698 "topology": "\"circular\""
649 }, 699 },
650 "state": "ok", 700 "state": "ok",
651 "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", 701 "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",
652 "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", 702 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
653 "tool_id": "cloning_simulation", 703 "tool_id": "cloning_simulation",
654 "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", 704 "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",
655 "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", 705 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
656 "update_time": "2025-05-16T08:55:47.617074", 706 "update_time": "2025-05-16T12:36:54.097489",
657 "user_email": "planemo@galaxyproject.org", 707 "user_email": "planemo@galaxyproject.org",
658 "user_id": "1d1943aa60deb628" 708 "user_id": "a7025157dd5d3039"
659 }, 709 },
660 "status": "success", 710 "status": "success",
661 "test_index": 2, 711 "test_index": 2,
662 "time_seconds": 24.352636098861694, 712 "time_seconds": 22.133039951324463,
663 "tool_id": "cloning_simulation", 713 "tool_id": "cloning_simulation",
664 "tool_version": "0.1.0+galaxy0" 714 "tool_version": "0.1.0+galaxy0"
665 }, 715 },
666 "has_data": true, 716 "has_data": true,
667 "id": "cloning_simulation-2" 717 "id": "cloning_simulation-2"
669 { 719 {
670 "data": { 720 "data": {
671 "inputs": { 721 "inputs": {
672 "adv|use_file_names_as_ids": true, 722 "adv|use_file_names_as_ids": true,
673 "assembly_csv": { 723 "assembly_csv": {
674 "id": "c4d206bede85e5c1", 724 "id": "df13d5ca39cba7c4",
675 "src": "hda" 725 "src": "hda"
676 }, 726 },
677 "assembly_plan_name": "BASICAssembly", 727 "assembly_plan_name": "BASICAssembly",
678 "genbank_files": { 728 "genbank_files": {
679 "id": "248d7f69d2402068", 729 "id": "edce0bc0654ca8cc",
680 "src": "hdca" 730 "src": "hdca"
681 }, 731 },
682 "topology": "circular" 732 "topology": "circular"
683 }, 733 },
684 "job": { 734 "job": {
685 "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'", 735 "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'",
686 "command_version": "", 736 "command_version": "",
687 "copied_from_job_id": null, 737 "copied_from_job_id": null,
688 "create_time": "2025-05-16T08:56:09.388287", 738 "create_time": "2025-05-16T12:37:15.245845",
689 "dependencies": [], 739 "dependencies": [
740 {
741 "cacheable": false,
742 "dependency_resolver": {
743 "auto_init": true,
744 "auto_install": true,
745 "can_uninstall_dependencies": true,
746 "ensure_channels": "conda-forge,bioconda",
747 "model_class": "CondaDependencyResolver",
748 "prefix": "/home/rkhaled/miniconda3",
749 "read_only": false,
750 "resolver_type": "conda",
751 "resolves_simple_dependencies": true,
752 "use_local": false,
753 "versionless": false
754 },
755 "dependency_type": "conda",
756 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
757 "exact": true,
758 "model_class": "MergedCondaDependency",
759 "name": "flametree",
760 "version": "0.1.11"
761 },
762 {
763 "cacheable": false,
764 "dependency_resolver": {
765 "auto_init": true,
766 "auto_install": true,
767 "can_uninstall_dependencies": true,
768 "ensure_channels": "conda-forge,bioconda",
769 "model_class": "CondaDependencyResolver",
770 "prefix": "/home/rkhaled/miniconda3",
771 "read_only": false,
772 "resolver_type": "conda",
773 "resolves_simple_dependencies": true,
774 "use_local": false,
775 "versionless": false
776 },
777 "dependency_type": "conda",
778 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
779 "exact": true,
780 "model_class": "MergedCondaDependency",
781 "name": "biopython",
782 "version": "1.85"
783 },
784 {
785 "cacheable": false,
786 "dependency_resolver": {
787 "auto_init": true,
788 "auto_install": true,
789 "can_uninstall_dependencies": true,
790 "ensure_channels": "conda-forge,bioconda",
791 "model_class": "CondaDependencyResolver",
792 "prefix": "/home/rkhaled/miniconda3",
793 "read_only": false,
794 "resolver_type": "conda",
795 "resolves_simple_dependencies": true,
796 "use_local": false,
797 "versionless": false
798 },
799 "dependency_type": "conda",
800 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
801 "exact": true,
802 "model_class": "MergedCondaDependency",
803 "name": "proglog",
804 "version": "0.1.10"
805 },
806 {
807 "cacheable": false,
808 "dependency_resolver": {
809 "auto_init": true,
810 "auto_install": true,
811 "can_uninstall_dependencies": true,
812 "ensure_channels": "conda-forge,bioconda",
813 "model_class": "CondaDependencyResolver",
814 "prefix": "/home/rkhaled/miniconda3",
815 "read_only": false,
816 "resolver_type": "conda",
817 "resolves_simple_dependencies": true,
818 "use_local": false,
819 "versionless": false
820 },
821 "dependency_type": "conda",
822 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
823 "exact": true,
824 "model_class": "MergedCondaDependency",
825 "name": "pandas",
826 "version": "2.2.3"
827 },
828 {
829 "cacheable": false,
830 "dependency_resolver": {
831 "auto_init": true,
832 "auto_install": true,
833 "can_uninstall_dependencies": true,
834 "ensure_channels": "conda-forge,bioconda",
835 "model_class": "CondaDependencyResolver",
836 "prefix": "/home/rkhaled/miniconda3",
837 "read_only": false,
838 "resolver_type": "conda",
839 "resolves_simple_dependencies": true,
840 "use_local": false,
841 "versionless": false
842 },
843 "dependency_type": "conda",
844 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
845 "exact": true,
846 "model_class": "MergedCondaDependency",
847 "name": "dnacauldron",
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850 {
851 "cacheable": false,
852 "dependency_resolver": {
853 "auto_init": true,
854 "auto_install": true,
855 "can_uninstall_dependencies": true,
856 "ensure_channels": "conda-forge,bioconda",
857 "model_class": "CondaDependencyResolver",
858 "prefix": "/home/rkhaled/miniconda3",
859 "read_only": false,
860 "resolver_type": "conda",
861 "resolves_simple_dependencies": true,
862 "use_local": false,
863 "versionless": false
864 },
865 "dependency_type": "conda",
866 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
867 "exact": true,
868 "model_class": "MergedCondaDependency",
869 "name": "pdf-reports",
870 "version": "0.3.9"
871 },
872 {
873 "cacheable": false,
874 "dependency_resolver": {
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876 "auto_install": true,
877 "can_uninstall_dependencies": true,
878 "ensure_channels": "conda-forge,bioconda",
879 "model_class": "CondaDependencyResolver",
880 "prefix": "/home/rkhaled/miniconda3",
881 "read_only": false,
882 "resolver_type": "conda",
883 "resolves_simple_dependencies": true,
884 "use_local": false,
885 "versionless": false
886 },
887 "dependency_type": "conda",
888 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
889 "exact": true,
890 "model_class": "MergedCondaDependency",
891 "name": "sequenticon",
892 "version": "0.1.8"
893 },
894 {
895 "cacheable": false,
896 "dependency_resolver": {
897 "auto_init": true,
898 "auto_install": true,
899 "can_uninstall_dependencies": true,
900 "ensure_channels": "conda-forge,bioconda",
901 "model_class": "CondaDependencyResolver",
902 "prefix": "/home/rkhaled/miniconda3",
903 "read_only": false,
904 "resolver_type": "conda",
905 "resolves_simple_dependencies": true,
906 "use_local": false,
907 "versionless": false
908 },
909 "dependency_type": "conda",
910 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
911 "exact": true,
912 "model_class": "MergedCondaDependency",
913 "name": "dna_features_viewer",
914 "version": "3.1.5"
915 }
916 ],
690 "exit_code": 0, 917 "exit_code": 0,
691 "external_id": "70839", 918 "external_id": "206517",
692 "galaxy_version": "24.2", 919 "galaxy_version": "24.2",
693 "handler": null, 920 "handler": null,
694 "history_id": "248d7f69d2402068", 921 "history_id": "4dd0eedec5562f6e",
695 "id": "ecaf8d4d1aeb8c86", 922 "id": "920c0db56b0a806b",
696 "inputs": { 923 "inputs": {
697 "assembly_csv": { 924 "assembly_csv": {
698 "id": "c4d206bede85e5c1", 925 "id": "df13d5ca39cba7c4",
699 "src": "hda", 926 "src": "hda",
700 "uuid": "ed3f4797-0002-46e3-a245-70ec97e59118" 927 "uuid": "e971a6cf-b13e-4a65-a78d-aa22a0ea1fff"
701 }, 928 },
702 "genbank_files1": { 929 "genbank_files1": {
703 "id": "065a19c3622776e9", 930 "id": "caecbbc14917ac69",
704 "src": "hda", 931 "src": "hda",
705 "uuid": "09dd12f1-a528-4e2a-a1d3-b9b57e7a02a2" 932 "uuid": "4f0d4258-2f50-4a4e-9271-58e8c272856e"
706 }, 933 },
707 "genbank_files2": { 934 "genbank_files2": {
708 "id": "ac67f4a6521db48c", 935 "id": "10cd084c8017547c",
709 "src": "hda", 936 "src": "hda",
710 "uuid": "be63c5f6-6c15-43c9-a467-0f00c3395bcf" 937 "uuid": "27f67c7a-5e38-4103-a00b-a9d8234b6686"
711 }, 938 },
712 "genbank_files3": { 939 "genbank_files3": {
713 "id": "77ed38528f61eafd", 940 "id": "aa3451be0c94f76e",
714 "src": "hda", 941 "src": "hda",
715 "uuid": "2e03930b-3e9f-45be-9750-42560f39cf14" 942 "uuid": "4e880afa-3f37-43a4-982e-36d750aab3d3"
716 }, 943 },
717 "genbank_files4": { 944 "genbank_files4": {
718 "id": "626b9fd2eae5943c", 945 "id": "a5f159065ae97d01",
719 "src": "hda", 946 "src": "hda",
720 "uuid": "5bdbe27f-640f-4db1-bc7b-fcedf4b2737a" 947 "uuid": "3746bcc6-ee0c-4936-832f-ce29f808430d"
721 }, 948 },
722 "genbank_files5": { 949 "genbank_files5": {
723 "id": "4a4771cb4e71e8ed", 950 "id": "a001a939426dadd1",
724 "src": "hda", 951 "src": "hda",
725 "uuid": "cd53d85a-7ced-4da5-bc73-eb4b74a200e3" 952 "uuid": "788ebd7b-6247-4f96-a3d3-3c3306c210a0"
726 } 953 }
727 }, 954 },
728 "job_messages": [], 955 "job_messages": [],
729 "job_metrics": [], 956 "job_metrics": [],
730 "job_runner_name": null, 957 "job_runner_name": null,
731 "job_stderr": "", 958 "job_stderr": "",
732 "job_stdout": "", 959 "job_stdout": "",
733 "model_class": "Job", 960 "model_class": "Job",
734 "output_collections": {}, 961 "output_collections": {
962 "construct_gb": {
963 "id": "052d0d471d180256",
964 "src": "hdca"
965 }
966 },
735 "outputs": { 967 "outputs": {
736 "output_zip": { 968 "output_zip": {
737 "id": "ecaf8d4d1aeb8c86", 969 "id": "081ab14c99ce168b",
738 "src": "hda", 970 "src": "hda",
739 "uuid": "2ce9e85d-d4e7-4104-833f-9fcac95e2c6d" 971 "uuid": "5e0faa51-141c-49d1-ba84-ca8aba27508c"
740 } 972 }
741 }, 973 },
742 "params": { 974 "params": {
743 "__input_ext": "\"input\"", 975 "__input_ext": "\"input\"",
744 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 976 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
745 "assembly_plan_name": "\"BASICAssembly\"", 977 "assembly_plan_name": "\"BASICAssembly\"",
746 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 978 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
747 "dbkey": "\"?\"", 979 "dbkey": "\"?\"",
748 "domesticated_input": null, 980 "domesticated_input": null,
749 "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}", 981 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
750 "topology": "\"circular\"" 982 "topology": "\"circular\""
751 }, 983 },
752 "state": "ok", 984 "state": "ok",
753 "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", 985 "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",
754 "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", 986 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
755 "tool_id": "cloning_simulation", 987 "tool_id": "cloning_simulation",
756 "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", 988 "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",
757 "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", 989 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
758 "update_time": "2025-05-16T08:56:20.015826", 990 "update_time": "2025-05-16T12:37:25.925491",
759 "user_email": "planemo@galaxyproject.org", 991 "user_email": "planemo@galaxyproject.org",
760 "user_id": "1d1943aa60deb628" 992 "user_id": "a7025157dd5d3039"
761 }, 993 },
762 "status": "success", 994 "status": "success",
763 "test_index": 3, 995 "test_index": 3,
764 "time_seconds": 32.09558367729187, 996 "time_seconds": 31.832648515701294,
765 "tool_id": "cloning_simulation", 997 "tool_id": "cloning_simulation",
766 "tool_version": "0.1.0+galaxy0" 998 "tool_version": "0.1.0+galaxy0"
767 }, 999 },
768 "has_data": true, 1000 "has_data": true,
769 "id": "cloning_simulation-3" 1001 "id": "cloning_simulation-3"
771 { 1003 {
772 "data": { 1004 "data": {
773 "inputs": { 1005 "inputs": {
774 "adv|use_file_names_as_ids": true, 1006 "adv|use_file_names_as_ids": true,
775 "assembly_csv": { 1007 "assembly_csv": {
776 "id": "1b325227d95fdc76", 1008 "id": "6af8c0d3c72d39ba",
777 "src": "hda" 1009 "src": "hda"
778 }, 1010 },
779 "assembly_plan_name": "BioBrickStandardAssembly", 1011 "assembly_plan_name": "BioBrickStandardAssembly",
780 "genbank_files": { 1012 "genbank_files": {
781 "id": "a363c57bce5ddac4", 1013 "id": "5827a0347340e98b",
782 "src": "hdca" 1014 "src": "hdca"
783 }, 1015 },
784 "topology": "circular" 1016 "topology": "circular"
785 }, 1017 },
786 "job": { 1018 "job": {
787 "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'", 1019 "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'",
788 "command_version": "", 1020 "command_version": "",
789 "copied_from_job_id": null, 1021 "copied_from_job_id": null,
790 "create_time": "2025-05-16T08:56:41.646034", 1022 "create_time": "2025-05-16T12:37:47.708969",
791 "dependencies": [ 1023 "dependencies": [
792 { 1024 {
793 "cacheable": false, 1025 "cacheable": false,
794 "dependency_resolver": { 1026 "dependency_resolver": {
795 "auto_init": true, 1027 "auto_init": true,
803 "resolves_simple_dependencies": true, 1035 "resolves_simple_dependencies": true,
804 "use_local": false, 1036 "use_local": false,
805 "versionless": false 1037 "versionless": false
806 }, 1038 },
807 "dependency_type": "conda", 1039 "dependency_type": "conda",
808 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1040 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
809 "exact": true, 1041 "exact": true,
810 "model_class": "MergedCondaDependency", 1042 "model_class": "MergedCondaDependency",
811 "name": "flametree", 1043 "name": "flametree",
812 "version": "0.1.11" 1044 "version": "0.1.11"
813 }, 1045 },
825 "resolves_simple_dependencies": true, 1057 "resolves_simple_dependencies": true,
826 "use_local": false, 1058 "use_local": false,
827 "versionless": false 1059 "versionless": false
828 }, 1060 },
829 "dependency_type": "conda", 1061 "dependency_type": "conda",
830 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1062 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
831 "exact": true, 1063 "exact": true,
832 "model_class": "MergedCondaDependency", 1064 "model_class": "MergedCondaDependency",
833 "name": "biopython", 1065 "name": "biopython",
834 "version": "1.85" 1066 "version": "1.85"
835 }, 1067 },
847 "resolves_simple_dependencies": true, 1079 "resolves_simple_dependencies": true,
848 "use_local": false, 1080 "use_local": false,
849 "versionless": false 1081 "versionless": false
850 }, 1082 },
851 "dependency_type": "conda", 1083 "dependency_type": "conda",
852 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1084 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
853 "exact": true, 1085 "exact": true,
854 "model_class": "MergedCondaDependency", 1086 "model_class": "MergedCondaDependency",
855 "name": "proglog", 1087 "name": "proglog",
856 "version": "0.1.10" 1088 "version": "0.1.10"
857 }, 1089 },
869 "resolves_simple_dependencies": true, 1101 "resolves_simple_dependencies": true,
870 "use_local": false, 1102 "use_local": false,
871 "versionless": false 1103 "versionless": false
872 }, 1104 },
873 "dependency_type": "conda", 1105 "dependency_type": "conda",
874 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1106 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
875 "exact": true, 1107 "exact": true,
876 "model_class": "MergedCondaDependency", 1108 "model_class": "MergedCondaDependency",
877 "name": "pandas", 1109 "name": "pandas",
878 "version": "2.2.3" 1110 "version": "2.2.3"
879 }, 1111 },
891 "resolves_simple_dependencies": true, 1123 "resolves_simple_dependencies": true,
892 "use_local": false, 1124 "use_local": false,
893 "versionless": false 1125 "versionless": false
894 }, 1126 },
895 "dependency_type": "conda", 1127 "dependency_type": "conda",
896 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1128 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
897 "exact": true, 1129 "exact": true,
898 "model_class": "MergedCondaDependency", 1130 "model_class": "MergedCondaDependency",
899 "name": "dnacauldron", 1131 "name": "dnacauldron",
900 "version": "2.0.12" 1132 "version": "2.0.12"
901 }, 1133 },
913 "resolves_simple_dependencies": true, 1145 "resolves_simple_dependencies": true,
914 "use_local": false, 1146 "use_local": false,
915 "versionless": false 1147 "versionless": false
916 }, 1148 },
917 "dependency_type": "conda", 1149 "dependency_type": "conda",
918 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1150 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
919 "exact": true, 1151 "exact": true,
920 "model_class": "MergedCondaDependency", 1152 "model_class": "MergedCondaDependency",
921 "name": "pdf-reports", 1153 "name": "pdf-reports",
922 "version": "0.3.9" 1154 "version": "0.3.9"
923 }, 1155 },
935 "resolves_simple_dependencies": true, 1167 "resolves_simple_dependencies": true,
936 "use_local": false, 1168 "use_local": false,
937 "versionless": false 1169 "versionless": false
938 }, 1170 },
939 "dependency_type": "conda", 1171 "dependency_type": "conda",
940 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1172 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
941 "exact": true, 1173 "exact": true,
942 "model_class": "MergedCondaDependency", 1174 "model_class": "MergedCondaDependency",
943 "name": "sequenticon", 1175 "name": "sequenticon",
944 "version": "0.1.8" 1176 "version": "0.1.8"
945 }, 1177 },
957 "resolves_simple_dependencies": true, 1189 "resolves_simple_dependencies": true,
958 "use_local": false, 1190 "use_local": false,
959 "versionless": false 1191 "versionless": false
960 }, 1192 },
961 "dependency_type": "conda", 1193 "dependency_type": "conda",
962 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1194 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
963 "exact": true, 1195 "exact": true,
964 "model_class": "MergedCondaDependency", 1196 "model_class": "MergedCondaDependency",
965 "name": "dna_features_viewer", 1197 "name": "dna_features_viewer",
966 "version": "3.1.4" 1198 "version": "3.1.5"
967 } 1199 }
968 ], 1200 ],
969 "exit_code": 0, 1201 "exit_code": 0,
970 "external_id": "71459", 1202 "external_id": "207114",
971 "galaxy_version": "24.2", 1203 "galaxy_version": "24.2",
972 "handler": null, 1204 "handler": null,
973 "history_id": "a363c57bce5ddac4", 1205 "history_id": "d1cbd0905c1fc860",
974 "id": "4d500d87322140a3", 1206 "id": "081ab14c99ce168b",
975 "inputs": { 1207 "inputs": {
976 "assembly_csv": { 1208 "assembly_csv": {
977 "id": "1b325227d95fdc76", 1209 "id": "6af8c0d3c72d39ba",
978 "src": "hda", 1210 "src": "hda",
979 "uuid": "7e6259bf-8646-4691-b40d-d91bbe52d6c5" 1211 "uuid": "4ed60503-3b9f-4204-a8e9-0b96f76b1e49"
980 }, 1212 },
981 "genbank_files1": { 1213 "genbank_files1": {
982 "id": "2d4530cd892a2a69", 1214 "id": "06bb6ed11a5684d2",
983 "src": "hda", 1215 "src": "hda",
984 "uuid": "48f246fb-df3d-4c65-a99e-cc314c9a2d20" 1216 "uuid": "773be428-2d30-4b95-9894-d3758634a3d0"
985 }, 1217 },
986 "genbank_files2": { 1218 "genbank_files2": {
987 "id": "afd885e9dc2aeeee", 1219 "id": "f34ce69b933b349e",
988 "src": "hda", 1220 "src": "hda",
989 "uuid": "50cb308d-4eb5-4d9d-ae07-011179d84b2e" 1221 "uuid": "bac673f5-074c-4810-9949-59d3b228d83c"
990 }, 1222 },
991 "genbank_files3": { 1223 "genbank_files3": {
992 "id": "ae8033db013a49b9", 1224 "id": "c295924a5ace6ae8",
993 "src": "hda", 1225 "src": "hda",
994 "uuid": "13b514d1-710c-46ef-9b83-939acad72375" 1226 "uuid": "e5b8dfd0-6e81-47e4-b899-08976d0a1724"
995 }, 1227 },
996 "genbank_files4": { 1228 "genbank_files4": {
997 "id": "0661f11e9507b8a6", 1229 "id": "f3a950b5ccc2e145",
998 "src": "hda", 1230 "src": "hda",
999 "uuid": "30bef7c3-fecb-40f7-b435-daf794d456c1" 1231 "uuid": "158cbebb-69fc-4333-b783-e9171b5324d6"
1000 }, 1232 },
1001 "genbank_files5": { 1233 "genbank_files5": {
1002 "id": "fcc678ee7e8e9f81", 1234 "id": "486d488c3f12b41a",
1003 "src": "hda", 1235 "src": "hda",
1004 "uuid": "a87d7ba7-2092-45e2-9aff-813bb53a02a6" 1236 "uuid": "a5b6ae8b-1068-416f-b0ac-1c44e299cb87"
1005 } 1237 }
1006 }, 1238 },
1007 "job_messages": [], 1239 "job_messages": [],
1008 "job_metrics": [], 1240 "job_metrics": [],
1009 "job_runner_name": null, 1241 "job_runner_name": null,
1010 "job_stderr": "", 1242 "job_stderr": "",
1011 "job_stdout": "", 1243 "job_stdout": "",
1012 "model_class": "Job", 1244 "model_class": "Job",
1013 "output_collections": {}, 1245 "output_collections": {
1246 "construct_gb": {
1247 "id": "26800a0030991202",
1248 "src": "hdca"
1249 }
1250 },
1014 "outputs": { 1251 "outputs": {
1252 "__new_primary_file_construct_gb|C1_prom_barcode__": {
1253 "id": "62952fe061c1d5d6",
1254 "src": "hda",
1255 "uuid": "fb185bc3-4c8e-4095-864e-edc42d8c87ab"
1256 },
1257 "__new_primary_file_construct_gb|C2_gfp_term__": {
1258 "id": "14c055702e438446",
1259 "src": "hda",
1260 "uuid": "cb6310a2-1237-4f80-9efa-f149cb896f4d"
1261 },
1262 "__new_primary_file_construct_gb|C3_final__": {
1263 "id": "e9ef3e2f0e439cf2",
1264 "src": "hda",
1265 "uuid": "13db93e9-4505-4542-845c-57029b5e9a89"
1266 },
1015 "output_zip": { 1267 "output_zip": {
1016 "id": "4d500d87322140a3", 1268 "id": "7f1cb49d27c5ee0d",
1017 "src": "hda", 1269 "src": "hda",
1018 "uuid": "664a6a95-4ce6-4f74-be51-728a9cbd55da" 1270 "uuid": "5776ccd7-5dca-4f21-b288-9c15a0b9cdca"
1019 } 1271 }
1020 }, 1272 },
1021 "params": { 1273 "params": {
1022 "__input_ext": "\"input\"", 1274 "__input_ext": "\"input\"",
1023 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1275 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1024 "assembly_plan_name": "\"BioBrickStandardAssembly\"", 1276 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
1025 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1277 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1026 "dbkey": "\"?\"", 1278 "dbkey": "\"?\"",
1027 "domesticated_input": null, 1279 "domesticated_input": null,
1028 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", 1280 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
1029 "topology": "\"circular\"" 1281 "topology": "\"circular\""
1030 }, 1282 },
1031 "state": "ok", 1283 "state": "ok",
1032 "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", 1284 "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",
1033 "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", 1285 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
1034 "tool_id": "cloning_simulation", 1286 "tool_id": "cloning_simulation",
1035 "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", 1287 "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",
1036 "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", 1288 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
1037 "update_time": "2025-05-16T08:56:55.140287", 1289 "update_time": "2025-05-16T12:38:00.688550",
1038 "user_email": "planemo@galaxyproject.org", 1290 "user_email": "planemo@galaxyproject.org",
1039 "user_id": "1d1943aa60deb628" 1291 "user_id": "a7025157dd5d3039"
1040 }, 1292 },
1041 "status": "success", 1293 "status": "success",
1042 "test_index": 4, 1294 "test_index": 4,
1043 "time_seconds": 34.888214349746704, 1295 "time_seconds": 34.85270929336548,
1044 "tool_id": "cloning_simulation", 1296 "tool_id": "cloning_simulation",
1045 "tool_version": "0.1.0+galaxy0" 1297 "tool_version": "0.1.0+galaxy0"
1046 }, 1298 },
1047 "has_data": true, 1299 "has_data": true,
1048 "id": "cloning_simulation-4" 1300 "id": "cloning_simulation-4"
1050 { 1302 {
1051 "data": { 1303 "data": {
1052 "inputs": { 1304 "inputs": {
1053 "adv|use_file_names_as_ids": true, 1305 "adv|use_file_names_as_ids": true,
1054 "assembly_csv": { 1306 "assembly_csv": {
1055 "id": "a727d841eabfe479", 1307 "id": "4e0765e9771b7fbe",
1056 "src": "hda" 1308 "src": "hda"
1057 }, 1309 },
1058 "assembly_plan_name": "Type2sRestrictionAssembly", 1310 "assembly_plan_name": "Type2sRestrictionAssembly",
1059 "domesticated_input": { 1311 "domesticated_input": {
1060 "id": "8ab843ac4a5890da", 1312 "id": "9e9c740782c078df",
1061 "src": "hdca" 1313 "src": "hdca"
1062 }, 1314 },
1063 "genbank_files": { 1315 "genbank_files": {
1064 "id": "6206f91299006d13", 1316 "id": "d70a40a14f24deac",
1065 "src": "hdca" 1317 "src": "hdca"
1066 }, 1318 },
1067 "topology": "circular" 1319 "topology": "circular"
1068 }, 1320 },
1069 "job": { 1321 "job": {
1070 "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'", 1322 "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'",
1071 "command_version": "", 1323 "command_version": "",
1072 "copied_from_job_id": null, 1324 "copied_from_job_id": null,
1073 "create_time": "2025-05-16T08:57:35.145295", 1325 "create_time": "2025-05-16T12:38:41.107674",
1074 "dependencies": [ 1326 "dependencies": [
1075 { 1327 {
1076 "cacheable": false, 1328 "cacheable": false,
1077 "dependency_resolver": { 1329 "dependency_resolver": {
1078 "auto_init": true, 1330 "auto_init": true,
1086 "resolves_simple_dependencies": true, 1338 "resolves_simple_dependencies": true,
1087 "use_local": false, 1339 "use_local": false,
1088 "versionless": false 1340 "versionless": false
1089 }, 1341 },
1090 "dependency_type": "conda", 1342 "dependency_type": "conda",
1091 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1343 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1092 "exact": true, 1344 "exact": true,
1093 "model_class": "MergedCondaDependency", 1345 "model_class": "MergedCondaDependency",
1094 "name": "flametree", 1346 "name": "flametree",
1095 "version": "0.1.11" 1347 "version": "0.1.11"
1096 }, 1348 },
1108 "resolves_simple_dependencies": true, 1360 "resolves_simple_dependencies": true,
1109 "use_local": false, 1361 "use_local": false,
1110 "versionless": false 1362 "versionless": false
1111 }, 1363 },
1112 "dependency_type": "conda", 1364 "dependency_type": "conda",
1113 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1365 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1114 "exact": true, 1366 "exact": true,
1115 "model_class": "MergedCondaDependency", 1367 "model_class": "MergedCondaDependency",
1116 "name": "biopython", 1368 "name": "biopython",
1117 "version": "1.85" 1369 "version": "1.85"
1118 }, 1370 },
1130 "resolves_simple_dependencies": true, 1382 "resolves_simple_dependencies": true,
1131 "use_local": false, 1383 "use_local": false,
1132 "versionless": false 1384 "versionless": false
1133 }, 1385 },
1134 "dependency_type": "conda", 1386 "dependency_type": "conda",
1135 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1387 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1136 "exact": true, 1388 "exact": true,
1137 "model_class": "MergedCondaDependency", 1389 "model_class": "MergedCondaDependency",
1138 "name": "proglog", 1390 "name": "proglog",
1139 "version": "0.1.10" 1391 "version": "0.1.10"
1140 }, 1392 },
1152 "resolves_simple_dependencies": true, 1404 "resolves_simple_dependencies": true,
1153 "use_local": false, 1405 "use_local": false,
1154 "versionless": false 1406 "versionless": false
1155 }, 1407 },
1156 "dependency_type": "conda", 1408 "dependency_type": "conda",
1157 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1409 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1158 "exact": true, 1410 "exact": true,
1159 "model_class": "MergedCondaDependency", 1411 "model_class": "MergedCondaDependency",
1160 "name": "pandas", 1412 "name": "pandas",
1161 "version": "2.2.3" 1413 "version": "2.2.3"
1162 }, 1414 },
1174 "resolves_simple_dependencies": true, 1426 "resolves_simple_dependencies": true,
1175 "use_local": false, 1427 "use_local": false,
1176 "versionless": false 1428 "versionless": false
1177 }, 1429 },
1178 "dependency_type": "conda", 1430 "dependency_type": "conda",
1179 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1431 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1180 "exact": true, 1432 "exact": true,
1181 "model_class": "MergedCondaDependency", 1433 "model_class": "MergedCondaDependency",
1182 "name": "dnacauldron", 1434 "name": "dnacauldron",
1183 "version": "2.0.12" 1435 "version": "2.0.12"
1184 }, 1436 },
1196 "resolves_simple_dependencies": true, 1448 "resolves_simple_dependencies": true,
1197 "use_local": false, 1449 "use_local": false,
1198 "versionless": false 1450 "versionless": false
1199 }, 1451 },
1200 "dependency_type": "conda", 1452 "dependency_type": "conda",
1201 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1453 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1202 "exact": true, 1454 "exact": true,
1203 "model_class": "MergedCondaDependency", 1455 "model_class": "MergedCondaDependency",
1204 "name": "pdf-reports", 1456 "name": "pdf-reports",
1205 "version": "0.3.9" 1457 "version": "0.3.9"
1206 }, 1458 },
1218 "resolves_simple_dependencies": true, 1470 "resolves_simple_dependencies": true,
1219 "use_local": false, 1471 "use_local": false,
1220 "versionless": false 1472 "versionless": false
1221 }, 1473 },
1222 "dependency_type": "conda", 1474 "dependency_type": "conda",
1223 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1475 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1224 "exact": true, 1476 "exact": true,
1225 "model_class": "MergedCondaDependency", 1477 "model_class": "MergedCondaDependency",
1226 "name": "sequenticon", 1478 "name": "sequenticon",
1227 "version": "0.1.8" 1479 "version": "0.1.8"
1228 }, 1480 },
1240 "resolves_simple_dependencies": true, 1492 "resolves_simple_dependencies": true,
1241 "use_local": false, 1493 "use_local": false,
1242 "versionless": false 1494 "versionless": false
1243 }, 1495 },
1244 "dependency_type": "conda", 1496 "dependency_type": "conda",
1245 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-414e7261396ae5d11be85675e1e19db222325018468f2829061591addd560be0", 1497 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1246 "exact": true, 1498 "exact": true,
1247 "model_class": "MergedCondaDependency", 1499 "model_class": "MergedCondaDependency",
1248 "name": "dna_features_viewer", 1500 "name": "dna_features_viewer",
1249 "version": "3.1.4" 1501 "version": "3.1.5"
1250 } 1502 }
1251 ], 1503 ],
1252 "exit_code": 0, 1504 "exit_code": 0,
1253 "external_id": "72541", 1505 "external_id": "208235",
1254 "galaxy_version": "24.2", 1506 "galaxy_version": "24.2",
1255 "handler": null, 1507 "handler": null,
1256 "history_id": "8ab843ac4a5890da", 1508 "history_id": "0494b81690cb2f5c",
1257 "id": "9d82ca4e11899647", 1509 "id": "1ad8534b5033158f",
1258 "inputs": { 1510 "inputs": {
1259 "assembly_csv": { 1511 "assembly_csv": {
1260 "id": "a727d841eabfe479", 1512 "id": "4e0765e9771b7fbe",
1261 "src": "hda", 1513 "src": "hda",
1262 "uuid": "4abb21a9-cb77-4f0c-9a76-3c01fd662d2a" 1514 "uuid": "c652bef1-f073-431c-9e5b-956a58e85d22"
1263 }, 1515 },
1264 "domesticated_input1": { 1516 "domesticated_input1": {
1265 "id": "3437b137460a9bf9", 1517 "id": "067523cf02b98b71",
1266 "src": "hda", 1518 "src": "hda",
1267 "uuid": "6a2287bd-1281-4c99-89a6-e4af944c272a" 1519 "uuid": "afe4126c-9cc0-45ec-a7d4-37816cb2132d"
1268 }, 1520 },
1269 "domesticated_input2": { 1521 "domesticated_input2": {
1270 "id": "4e00b6593169f669", 1522 "id": "2f0a34076d4435df",
1271 "src": "hda", 1523 "src": "hda",
1272 "uuid": "2c942443-9fa9-48a9-bf35-2f8c2258967b" 1524 "uuid": "fa8a7e9a-fa40-4e9f-a508-261fd8441292"
1273 }, 1525 },
1274 "domesticated_input3": { 1526 "domesticated_input3": {
1275 "id": "348e227de2cf9bbe", 1527 "id": "a12a625822f3f961",
1276 "src": "hda", 1528 "src": "hda",
1277 "uuid": "becfbff9-15f1-4830-b192-93e7892f371d" 1529 "uuid": "7ddb44a7-da6d-4215-8d11-1ba01c4f6516"
1278 }, 1530 },
1279 "domesticated_input4": { 1531 "domesticated_input4": {
1280 "id": "cb7d74ca0f50a91c", 1532 "id": "0b82bdc4f78225f4",
1281 "src": "hda", 1533 "src": "hda",
1282 "uuid": "876d6160-fcd5-49e1-ae58-aa8d30c94e09" 1534 "uuid": "bff58a1b-e69e-4cb4-b344-79ba8800ac03"
1283 }, 1535 },
1284 "domesticated_input5": { 1536 "domesticated_input5": {
1285 "id": "f0efc768d058218e", 1537 "id": "5c9f1017a9cfea44",
1286 "src": "hda", 1538 "src": "hda",
1287 "uuid": "3a81169d-4569-4c6d-9417-a3c5924f8649" 1539 "uuid": "af806691-7022-4bf2-a42b-7437042cee37"
1288 }, 1540 },
1289 "genbank_files1": { 1541 "genbank_files1": {
1290 "id": "4e56a0aaa45feaf7", 1542 "id": "db55fd2326eb05de",
1291 "src": "hda", 1543 "src": "hda",
1292 "uuid": "2b34f95b-2776-40a7-ac0a-abdb3d2b151f" 1544 "uuid": "bcd311aa-69db-4f2a-9d04-90f34cd78a6f"
1293 }, 1545 },
1294 "genbank_files2": { 1546 "genbank_files2": {
1295 "id": "cb872b8bb704ec40", 1547 "id": "551b1ccaf842a34c",
1296 "src": "hda", 1548 "src": "hda",
1297 "uuid": "81535329-42d0-4e9d-a713-beb8033e2db9" 1549 "uuid": "049931ba-600a-46d6-a73e-af6bd3f545e3"
1298 }, 1550 },
1299 "genbank_files3": { 1551 "genbank_files3": {
1300 "id": "90f63057cb36f606", 1552 "id": "aa4b51af1d3e5956",
1301 "src": "hda", 1553 "src": "hda",
1302 "uuid": "dbbc8408-63b6-4265-8878-94942c7b2016" 1554 "uuid": "860e934f-31f6-4ac6-9eac-fd3abf031b08"
1303 }, 1555 },
1304 "genbank_files4": { 1556 "genbank_files4": {
1305 "id": "efde02d124a713a2", 1557 "id": "1ad8534b5033158f",
1306 "src": "hda", 1558 "src": "hda",
1307 "uuid": "41d94b9c-f2f0-4253-88bb-896b26fdb7a0" 1559 "uuid": "aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21"
1308 }, 1560 },
1309 "genbank_files5": { 1561 "genbank_files5": {
1310 "id": "81a37b9282573f69", 1562 "id": "67e60392c24a116d",
1311 "src": "hda", 1563 "src": "hda",
1312 "uuid": "48a630fc-ea4b-4c19-8b0b-fb78db4bff7d" 1564 "uuid": "3d97e337-7388-4fab-a6c3-7cb99f371f84"
1313 }, 1565 },
1314 "genbank_files6": { 1566 "genbank_files6": {
1315 "id": "9989729bf7df579e", 1567 "id": "f0035bfbf96f19ca",
1316 "src": "hda", 1568 "src": "hda",
1317 "uuid": "459d85d8-4869-4d03-bd2a-d083e4ecf818" 1569 "uuid": "b45031f8-71da-4365-9560-b827aa1d6794"
1318 }, 1570 },
1319 "genbank_files7": { 1571 "genbank_files7": {
1320 "id": "bc2865f07ef20436", 1572 "id": "d2976cafec9acf3d",
1321 "src": "hda", 1573 "src": "hda",
1322 "uuid": "1b189627-18cd-4c7c-8d19-46371420574a" 1574 "uuid": "9e21455c-b124-4c01-8524-949ff16b570e"
1323 } 1575 }
1324 }, 1576 },
1325 "job_messages": [], 1577 "job_messages": [],
1326 "job_metrics": [], 1578 "job_metrics": [],
1327 "job_runner_name": null, 1579 "job_runner_name": null,
1328 "job_stderr": "", 1580 "job_stderr": "",
1329 "job_stdout": "", 1581 "job_stdout": "",
1330 "model_class": "Job", 1582 "model_class": "Job",
1331 "output_collections": {}, 1583 "output_collections": {
1584 "construct_gb": {
1585 "id": "c02153e44a10e06a",
1586 "src": "hdca"
1587 }
1588 },
1332 "outputs": { 1589 "outputs": {
1590 "__new_primary_file_construct_gb|construct_1__": {
1591 "id": "a3a16f375ef01612",
1592 "src": "hda",
1593 "uuid": "760d3bcc-0498-4f4a-9420-511468a0b0b3"
1594 },
1595 "__new_primary_file_construct_gb|construct_2__": {
1596 "id": "99e6c6e9665a5a56",
1597 "src": "hda",
1598 "uuid": "9836288d-70fb-464e-b565-90dc8f966379"
1599 },
1600 "__new_primary_file_construct_gb|construct_3__": {
1601 "id": "2d10fdf290562ab3",
1602 "src": "hda",
1603 "uuid": "cf0e5bca-9446-4574-b885-ab1636310493"
1604 },
1605 "__new_primary_file_construct_gb|construct_4__": {
1606 "id": "071f312ace6db7aa",
1607 "src": "hda",
1608 "uuid": "9e552d2e-e5f3-4163-b4b4-6351ec76f0d3"
1609 },
1333 "output_zip": { 1610 "output_zip": {
1334 "id": "9d82ca4e11899647", 1611 "id": "72a012487a44f1a3",
1335 "src": "hda", 1612 "src": "hda",
1336 "uuid": "891d2044-502b-4e4b-b394-575c9e42a36f" 1613 "uuid": "a88370aa-4d36-4867-b0d6-613cc59ed01a"
1337 } 1614 }
1338 }, 1615 },
1339 "params": { 1616 "params": {
1340 "__input_ext": "\"input\"", 1617 "__input_ext": "\"input\"",
1341 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1618 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1342 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 1619 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1343 "chromInfo": "\"/tmp/tmps36anksu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1620 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1344 "dbkey": "\"?\"", 1621 "dbkey": "\"?\"",
1345 "domesticated_input": "{\"values\": [{\"id\": 6, \"src\": \"hdca\"}]}", 1622 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}",
1346 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", 1623 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}",
1347 "topology": "\"circular\"" 1624 "topology": "\"circular\""
1348 }, 1625 },
1349 "state": "ok", 1626 "state": "ok",
1350 "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", 1627 "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",
1351 "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", 1628 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1352 "tool_id": "cloning_simulation", 1629 "tool_id": "cloning_simulation",
1353 "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", 1630 "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",
1354 "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", 1631 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1355 "update_time": "2025-05-16T08:57:47.925883", 1632 "update_time": "2025-05-16T12:38:53.803402",
1356 "user_email": "planemo@galaxyproject.org", 1633 "user_email": "planemo@galaxyproject.org",
1357 "user_id": "1d1943aa60deb628" 1634 "user_id": "a7025157dd5d3039"
1358 }, 1635 },
1359 "status": "success", 1636 "status": "success",
1360 "test_index": 5, 1637 "test_index": 5,
1361 "time_seconds": 52.77062439918518, 1638 "time_seconds": 52.96998858451843,
1362 "tool_id": "cloning_simulation", 1639 "tool_id": "cloning_simulation",
1363 "tool_version": "0.1.0+galaxy0" 1640 "tool_version": "0.1.0+galaxy0"
1364 }, 1641 },
1365 "has_data": true, 1642 "has_data": true,
1366 "id": "cloning_simulation-5" 1643 "id": "cloning_simulation-5"