Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 15:074a76e84b80 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 13:39:57 +0000 |
| parents | 16ccb36aa8e3 |
| children | fbb241adf6c2 |
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--- a/output.json Mon May 26 11:29:13 2025 +0000 +++ b/output.json Mon May 26 13:39:57 2025 +0000 @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "c173cff58a987f8f", + "id": "1e8e6749bc68d8e8", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "fcc5b7d13a1328f6", + "id": "e2ca7f14a85a8d44", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/2/b/d/dataset_2bdf436f-52cc-4c6e-afdb-3f051629900f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/4/6/5/dataset_465a53ab-8770-4514-a9b3-227f79646eb7.dat,/tmp/tmpc6lic4p9/files/a/e/2/dataset_ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa.dat,/tmp/tmpc6lic4p9/files/e/6/4/dataset_e64057b1-43b3-4788-8891-77bcd297223c.dat,/tmp/tmpc6lic4p9/files/1/d/1/dataset_1d1f9832-b58e-48c2-b1b3-6c3fb18e9890.dat,/tmp/tmpc6lic4p9/files/6/7/3/dataset_6732fc79-081e-4edf-bccc-a0087520172a.dat,/tmp/tmpc6lic4p9/files/b/1/7/dataset_b17c7a49-3121-4292-95ff-51891aa066d1.dat,/tmp/tmpc6lic4p9/files/2/8/1/dataset_2811f816-8532-4ddd-8e29-9a6ed7dad54e.dat,/tmp/tmpc6lic4p9/files/e/7/4/dataset_e74d0182-807e-40a8-b67a-ac088fc2e02c.dat,/tmp/tmpc6lic4p9/files/9/d/c/dataset_9dc55c98-4ab9-4272-a680-9b3129954367.dat,/tmp/tmpc6lic4p9/files/9/5/6/dataset_95699db9-77cf-4ae1-8454-4f255f3cb62a.dat,/tmp/tmpc6lic4p9/files/1/1/9/dataset_11979c28-82ee-43c4-9e43-f34cb541f96b.dat,/tmp/tmpc6lic4p9/files/3/f/5/dataset_3f53cb86-2d2b-429a-bf51-e276bbe393fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/4/6/5/dataset_465a53ab-8770-4514-a9b3-227f79646eb7.dat:part_A.gb,/tmp/tmpc6lic4p9/files/a/e/2/dataset_ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa.dat:part_B.gb,/tmp/tmpc6lic4p9/files/e/6/4/dataset_e64057b1-43b3-4788-8891-77bcd297223c.dat:part_C.gb,/tmp/tmpc6lic4p9/files/1/d/1/dataset_1d1f9832-b58e-48c2-b1b3-6c3fb18e9890.dat:part_D.gb,/tmp/tmpc6lic4p9/files/6/7/3/dataset_6732fc79-081e-4edf-bccc-a0087520172a.dat:part_E.gb,/tmp/tmpc6lic4p9/files/b/1/7/dataset_b17c7a49-3121-4292-95ff-51891aa066d1.dat:part_F.gb,/tmp/tmpc6lic4p9/files/2/8/1/dataset_2811f816-8532-4ddd-8e29-9a6ed7dad54e.dat:part_G.gb,/tmp/tmpc6lic4p9/files/e/7/4/dataset_e74d0182-807e-40a8-b67a-ac088fc2e02c.dat:part_H.gb,/tmp/tmpc6lic4p9/files/9/d/c/dataset_9dc55c98-4ab9-4272-a680-9b3129954367.dat:part_I.gb,/tmp/tmpc6lic4p9/files/9/5/6/dataset_95699db9-77cf-4ae1-8454-4f255f3cb62a.dat:part_J.gb,/tmp/tmpc6lic4p9/files/1/1/9/dataset_11979c28-82ee-43c4-9e43-f34cb541f96b.dat:part_K.gb,/tmp/tmpc6lic4p9/files/3/f/5/dataset_3f53cb86-2d2b-429a-bf51-e276bbe393fa.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/tmpc6lic4p9/job_working_directory/000/14/outputs/dataset_ac2d98e7-ff55-4a94-9e79-861b07d63528.dat' && echo DEBUG && ls 'outdir_gb'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/2/0/d/dataset_20d4061a-81e4-4915-a841-ae8aa595c7b4.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat:part_A.gb,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat:part_B.gb,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat:part_C.gb,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat:part_D.gb,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat:part_E.gb,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat:part_G.gb,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat:part_H.gb,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat:part_I.gb,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat:part_J.gb,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat:part_K.gb,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.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/tmpm1fyob3t/job_working_directory/000/14/outputs/dataset_64d1d8ac-32f0-4095-be30-22eee31e24a4.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:24:01.275241", + "create_time": "2025-05-26T12:02:32.643157", "dependencies": [], "exit_code": 0, - "external_id": "151844", + "external_id": "172939", "galaxy_version": "24.2", "handler": null, - "history_id": "fcc5b7d13a1328f6", - "id": "c9445e550eef23d0", + "history_id": "e2ca7f14a85a8d44", + "id": "a36db940f4513bd9", "inputs": { "assembly_csv": { - "id": "c173cff58a987f8f", + "id": "1e8e6749bc68d8e8", "src": "hda", - "uuid": "2bdf436f-52cc-4c6e-afdb-3f051629900f" + "uuid": "20d4061a-81e4-4915-a841-ae8aa595c7b4" }, "genbank_files1": { - "id": "fcc5b7d13a1328f6", + "id": "e2ca7f14a85a8d44", "src": "hda", - "uuid": "465a53ab-8770-4514-a9b3-227f79646eb7" + "uuid": "dd844d61-fc05-41d9-8179-21233649407d" }, "genbank_files10": { - "id": "cf75f655bb15877b", + "id": "fbec4a551130f847", "src": "hda", - "uuid": "95699db9-77cf-4ae1-8454-4f255f3cb62a" + "uuid": "b8fd4610-2f6d-475c-8405-8bf8c2bc0306" }, "genbank_files11": { - "id": "744832bdd7ccd728", + "id": "5bd8560352cb0b69", "src": "hda", - "uuid": "11979c28-82ee-43c4-9e43-f34cb541f96b" + "uuid": "09f4b020-4e7b-4939-b3ba-348f91cb92bc" }, "genbank_files12": { - "id": "855b83dd0dec8eab", + "id": "cb2fe7fb50f38553", "src": "hda", - "uuid": "3f53cb86-2d2b-429a-bf51-e276bbe393fa" + "uuid": "eb730263-9442-4dca-a2dc-34b1cae450d7" }, "genbank_files2": { - "id": "df00a2d9def0cc87", + "id": "62e98d1a229b6ef5", "src": "hda", - "uuid": "ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa" + "uuid": "cb2362f3-4b32-46cc-a227-dc15742bf9e7" }, "genbank_files3": { - "id": "d9e72a80becfe6e7", + "id": "f8fe24202fc5b2e5", "src": "hda", - "uuid": "e64057b1-43b3-4788-8891-77bcd297223c" + "uuid": "6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a" }, "genbank_files4": { - "id": "038c626e299361e9", + "id": "0d58e12bbe78a903", "src": "hda", - "uuid": "1d1f9832-b58e-48c2-b1b3-6c3fb18e9890" + "uuid": "33e804b2-0fbe-4844-9b5d-420e8a2db772" }, "genbank_files5": { - "id": "c7c3cd49f3337c1a", + "id": "3937d5ff7c0e1373", "src": "hda", - "uuid": "6732fc79-081e-4edf-bccc-a0087520172a" + "uuid": "2db3825c-538b-483f-b6ff-8dc4ecc03780" }, "genbank_files6": { - "id": "51c35891e43131e2", + "id": "473b1992d5f5b84f", "src": "hda", - "uuid": "b17c7a49-3121-4292-95ff-51891aa066d1" + "uuid": "048ee7ed-5f4c-41ef-aed4-f2cf975aac92" }, "genbank_files7": { - "id": "84db48b219855f4d", + "id": "9b5c1fe7a52a75e0", "src": "hda", - "uuid": "2811f816-8532-4ddd-8e29-9a6ed7dad54e" + "uuid": "c505c12e-7089-4a17-a605-4f11dad6f1d7" }, "genbank_files8": { - "id": "cf00b67a5455eb5a", + "id": "c32c50a47ebf8564", "src": "hda", - "uuid": "e74d0182-807e-40a8-b67a-ac088fc2e02c" + "uuid": "4912f12d-0842-46b7-8aaf-2a94a52f04f8" }, "genbank_files9": { - "id": "a3780ecc1a00a0d8", + "id": "5f035ce298b798b0", "src": "hda", - "uuid": "9dc55c98-4ab9-4272-a680-9b3129954367" + "uuid": "b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027" } }, "job_messages": [], @@ -108,60 +108,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "df00a2d9def0cc87", + "id": "62e98d1a229b6ef5", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "fedb85639c7c80b9", + "id": "182eefa577c2a56d", "src": "hda", - "uuid": "4bf90377-e4de-4d13-8ebc-39a53494ea2a" + "uuid": "991437a5-bbe4-4adb-8831-c9a871adb17f" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "bd75ec7b3d9705ea", + "id": "979fd704a8b37879", "src": "hda", - "uuid": "ac9bac0c-348b-46b7-a882-60f56867cc30" + "uuid": "9ebdb527-8609-4bc8-85a3-f8775156c356" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "7eb30039064fccdd", + "id": "b53ff5232a859d40", "src": "hda", - "uuid": "48e39545-a44e-410b-859b-01fcf6189002" + "uuid": "235361e4-93cc-4b56-ad81-c33ce8f593f0" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "61cc0a7b70456dfd", + "id": "1ce0e68b6cd95b3c", "src": "hda", - "uuid": "df8aca7f-8413-430f-b35f-7dac694ee0b6" + "uuid": "49100d5c-134b-4cb0-a86b-2cf03a336b1c" }, "output_zip": { - "id": "c9445e550eef23d0", + "id": "a36db940f4513bd9", "src": "hda", - "uuid": "ac2d98e7-ff55-4a94-9e79-861b07d63528" + "uuid": "64d1d8ac-32f0-4095-be30-22eee31e24a4" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.38it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.18it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/s, now=None]\r \r", - "stdout": " 1 2 3 4 5 6\n0 \nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.58it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/s, now=None]\r \r", + "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.38it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.18it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/s, now=None]\r \r", - "tool_stdout": " 1 2 3 4 5 6\n0 \nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n", - "update_time": "2025-05-26T11:24:14.526803", + "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, 2.58it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", + "update_time": "2025-05-26T12:02:45.106475", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 0, - "time_seconds": 53.70547914505005, + "time_seconds": 53.48332858085632, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -173,21 +173,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "3af58a5242e85ea6", + "id": "035124d32eef3033", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "d9e72a80becfe6e7", + "id": "f8fe24202fc5b2e5", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/1/d/6/dataset_1d624c24-e864-463a-9fd3-0c63fd46cbd2.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/5/0/5/dataset_505aafa2-5e9c-44bb-9d26-3f3e6248fc9b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/5/0/5/dataset_505aafa2-5e9c-44bb-9d26-3f3e6248fc9b.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/tmpc6lic4p9/job_working_directory/000/17/outputs/dataset_0f617192-e625-4d9e-8358-0b9b1b0aa024.dat' && echo DEBUG && ls 'outdir_gb'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/1/6/f/dataset_16f6d475-b614-4427-9c06-95a0d56d3c92.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.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/tmpm1fyob3t/job_working_directory/000/17/outputs/dataset_505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:24:25.394299", + "create_time": "2025-05-26T12:02:55.721992", "dependencies": [ { "cacheable": false, @@ -367,21 +367,21 @@ } ], "exit_code": 0, - "external_id": "152204", + "external_id": "173310", "galaxy_version": "24.2", "handler": null, - "history_id": "df00a2d9def0cc87", - "id": "7eb30039064fccdd", + "history_id": "62e98d1a229b6ef5", + "id": "b53ff5232a859d40", "inputs": { "assembly_csv": { - "id": "3af58a5242e85ea6", + "id": "035124d32eef3033", "src": "hda", - "uuid": "1d624c24-e864-463a-9fd3-0c63fd46cbd2" + "uuid": "16f6d475-b614-4427-9c06-95a0d56d3c92" }, "genbank_files1": { - "id": "3b85967b9c87a1cc", + "id": "1fe688df02a38cc2", "src": "hda", - "uuid": "505aafa2-5e9c-44bb-9d26-3f3e6248fc9b" + "uuid": "96a8f769-3544-4407-b064-04f24a733896" } }, "job_messages": [], @@ -392,55 +392,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "038c626e299361e9", + "id": "0d58e12bbe78a903", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "9773f41fb184880d", + "id": "f970a04054a49348", "src": "hda", - "uuid": "0d66c887-a6a3-4fd6-978a-9c0e2ce4b317" + "uuid": "ff8ea1a1-10ff-4416-b944-a78a4fd3e72e" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "41b44b0c750630a6", + "id": "ae9b306409c7f353", "src": "hda", - "uuid": "be7e7183-3b0d-40dd-9908-3e8dcd7f80bf" + "uuid": "7afee741-2c2b-4e3b-a947-819ebb5b67b4" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "bfc60c3d9bac68ee", + "id": "791483eeafbe6bcb", "src": "hda", - "uuid": "2c7f645c-33d1-4a91-9608-221494b22be4" + "uuid": "c820ba84-23dc-4e1c-b2de-abed54b17015" }, "output_zip": { - "id": "5c8c8c874b5b07c6", + "id": "cd80768c91dddfb6", "src": "hda", - "uuid": "0f617192-e625-4d9e-8358-0b9b1b0aa024" + "uuid": "505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.24it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.27it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.28it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.48it/s, now=None]\r \r", - "stdout": " 1 2 3 4 5\n0 \nconstruct parts NaN NaN NaN NaN\nconstruct_1 Frag_1 Frag_2 Frag_3 Frag_4 Frag_5\nconstruct_2 Frag_1 Frag_2 Frag_3 Frag_4b Frag_5\nconstruct_3 Frag_1 Frag_2 Frag_3 Frag_4c Frag_5b\nconstruct_4 Frag_1 Frag_2 Frag_3 Frag_4 NaN\nconstruct_5 Frag_1 Frag_2 Frag_3 Frag_4 Frag_4b\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\n", + "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.33it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.53it/s, now=None]\r \r", + "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.24it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.27it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.28it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.48it/s, now=None]\r \r", - "tool_stdout": " 1 2 3 4 5\n0 \nconstruct parts NaN NaN NaN NaN\nconstruct_1 Frag_1 Frag_2 Frag_3 Frag_4 Frag_5\nconstruct_2 Frag_1 Frag_2 Frag_3 Frag_4b Frag_5\nconstruct_3 Frag_1 Frag_2 Frag_3 Frag_4c Frag_5b\nconstruct_4 Frag_1 Frag_2 Frag_3 Frag_4 NaN\nconstruct_5 Frag_1 Frag_2 Frag_3 Frag_4 Frag_4b\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\n", - "update_time": "2025-05-26T11:24:37.446583", + "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, 4.35it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.33it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.53it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", + "update_time": "2025-05-26T12:03:07.748084", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 1, - "time_seconds": 22.626197814941406, + "time_seconds": 22.338457345962524, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -452,43 +452,220 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "48d1542b43af9171", + "id": "c9169186136d0f27", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "c7c3cd49f3337c1a", + "id": "3937d5ff7c0e1373", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/a/1/f/dataset_a1f989b9-e79f-4bd7-9cf3-66675c1d1e94.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/a/6/1/dataset_a617ae1f-70e3-4873-bdcc-f2268ffeaad4.dat,/tmp/tmpc6lic4p9/files/9/4/1/dataset_941b4e95-600a-485c-a3fa-1dcf0defdd76.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/a/6/1/dataset_a617ae1f-70e3-4873-bdcc-f2268ffeaad4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpc6lic4p9/files/9/4/1/dataset_941b4e95-600a-485c-a3fa-1dcf0defdd76.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/tmpc6lic4p9/job_working_directory/000/21/outputs/dataset_827e64a1-7f84-4f9e-8468-eabb3684efa3.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/7/c/dataset_f7c9ad78-8e74-4a3c-9579-80a93ac923de.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.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/tmpm1fyob3t/job_working_directory/000/21/outputs/dataset_3fc625c8-722f-4efb-9c09-0d664dec2a9d.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:24:49.729783", - "dependencies": [], + "create_time": "2025-05-26T12:03:18.983816", + "dependencies": [ + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "flametree", + "version": "0.1.11" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "biopython", + "version": "1.85" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "proglog", + "version": "0.1.10" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pandas", + "version": "2.2.3" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dnacauldron", + "version": "2.0.12" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "pdf-reports", + "version": "0.3.9" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "sequenticon", + "version": "0.1.8" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + "auto_install": true, + "can_uninstall_dependencies": true, + "ensure_channels": "conda-forge,bioconda", + "model_class": "CondaDependencyResolver", + "prefix": "/home/rkhaled/miniconda3", + "read_only": false, + "resolver_type": "conda", + "resolves_simple_dependencies": true, + "use_local": false, + "versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dna_features_viewer", + "version": "3.1.5" + } + ], "exit_code": 0, - "external_id": "152654", + "external_id": "173689", "galaxy_version": "24.2", "handler": null, - "history_id": "d9e72a80becfe6e7", - "id": "5c8c8c874b5b07c6", + "history_id": "f8fe24202fc5b2e5", + "id": "cd80768c91dddfb6", "inputs": { "assembly_csv": { - "id": "48d1542b43af9171", + "id": "c9169186136d0f27", "src": "hda", - "uuid": "a1f989b9-e79f-4bd7-9cf3-66675c1d1e94" + "uuid": "f7c9ad78-8e74-4a3c-9579-80a93ac923de" }, "genbank_files1": { - "id": "b8df5ed9fe071f18", + "id": "f14f22136515e5fc", "src": "hda", - "uuid": "a617ae1f-70e3-4873-bdcc-f2268ffeaad4" + "uuid": "f56913bd-fc92-4122-8cf1-d9b1c60e8385" }, "genbank_files2": { - "id": "6de9142d4b5ca725", + "id": "d00c2a698869e2f3", "src": "hda", - "uuid": "941b4e95-600a-485c-a3fa-1dcf0defdd76" + "uuid": "3b4e75b3-e6a6-459a-a959-d43ce00c3701" } }, "job_messages": [], @@ -499,40 +676,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "51c35891e43131e2", + "id": "473b1992d5f5b84f", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "56521fbfdcb4ef20", + "id": "0bb6e1adb7bbb7d6", "src": "hda", - "uuid": "827e64a1-7f84-4f9e-8468-eabb3684efa3" + "uuid": "3fc625c8-722f-4efb-9c09-0d664dec2a9d" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.16it/s, now=None]\r \r", - "stdout": " 1 ... 14\n0 ... \nConstruct1 RFP_GFP_BO_10232 ... p7_backbone\nConstruct2_flawed RFP_GFP_BO_10232 ... NaN\n\n[2 rows x 14 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.40it/s, now=None]\r \r", + "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.16it/s, now=None]\r \r", - "tool_stdout": " 1 ... 14\n0 ... \nConstruct1 RFP_GFP_BO_10232 ... p7_backbone\nConstruct2_flawed RFP_GFP_BO_10232 ... NaN\n\n[2 rows x 14 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T11:25:02.028309", + "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, 2.40it/s, now=None]\r \r", + "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", + "update_time": "2025-05-26T12:03:31.119796", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 2, - "time_seconds": 24.395533084869385, + "time_seconds": 23.440476655960083, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -544,21 +721,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "2b17a3fa18c23b8a", + "id": "b66a1bb5ed06a6bf", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { - "id": "84db48b219855f4d", + "id": "9b5c1fe7a52a75e0", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/6/b/e/dataset_6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/c/b/a/dataset_cba9b297-4dfe-4063-8510-6c48a1b6b7a1.dat,/tmp/tmpc6lic4p9/files/3/e/8/dataset_3e8dfce1-7a05-4665-9277-388e3aa42581.dat,/tmp/tmpc6lic4p9/files/a/5/d/dataset_a5d093c2-0087-453e-b7d1-d94a7cb664e0.dat,/tmp/tmpc6lic4p9/files/0/e/c/dataset_0ec72cc0-2a95-474b-aa77-7a436dad6a9b.dat,/tmp/tmpc6lic4p9/files/d/2/7/dataset_d272199f-2e1b-49e1-a597-5ffa11507e83.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/c/b/a/dataset_cba9b297-4dfe-4063-8510-6c48a1b6b7a1.dat:GFP.gb,/tmp/tmpc6lic4p9/files/3/e/8/dataset_3e8dfce1-7a05-4665-9277-388e3aa42581.dat:p15A_kan.gb,/tmp/tmpc6lic4p9/files/a/5/d/dataset_a5d093c2-0087-453e-b7d1-d94a7cb664e0.dat:promoter.gb,/tmp/tmpc6lic4p9/files/0/e/c/dataset_0ec72cc0-2a95-474b-aa77-7a436dad6a9b.dat:RFP.gb,/tmp/tmpc6lic4p9/files/d/2/7/dataset_d272199f-2e1b-49e1-a597-5ffa11507e83.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/tmpc6lic4p9/job_working_directory/000/28/outputs/dataset_7435335e-896e-47f4-89c7-3a6c2c25f247.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/b/4/dataset_fb426ceb-2615-447d-b04e-ae4253af648d.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat:GFP.gb,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat:p15A_kan.gb,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat:promoter.gb,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat:RFP.gb,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.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/tmpm1fyob3t/job_working_directory/000/28/outputs/dataset_45ef7ed5-48aa-4286-ac51-3391b593eb7c.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:25:23.055332", + "create_time": "2025-05-26T12:03:51.986652", "dependencies": [ { "cacheable": false, @@ -738,41 +915,41 @@ } ], "exit_code": 0, - "external_id": "153248", + "external_id": "174270", "galaxy_version": "24.2", "handler": null, - "history_id": "038c626e299361e9", - "id": "56521fbfdcb4ef20", + "history_id": "0d58e12bbe78a903", + "id": "0bb6e1adb7bbb7d6", "inputs": { "assembly_csv": { - "id": "2b17a3fa18c23b8a", + "id": "b66a1bb5ed06a6bf", "src": "hda", - "uuid": "6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc" + "uuid": "fb426ceb-2615-447d-b04e-ae4253af648d" }, "genbank_files1": { - "id": "aed8b1a22d89d8c9", + "id": "4c26f2b3928e5c2b", "src": "hda", - "uuid": "cba9b297-4dfe-4063-8510-6c48a1b6b7a1" + "uuid": "ecb057a2-dbf8-4105-b55e-d726ec1e9693" }, "genbank_files2": { - "id": "eba7a310b55aafdd", + "id": "7f1b25c57f1b4097", "src": "hda", - "uuid": "3e8dfce1-7a05-4665-9277-388e3aa42581" + "uuid": "498fe703-52c3-4162-be00-93f49f00689d" }, "genbank_files3": { - "id": "eca1089322e0a5fc", + "id": "cbd9b7f3981a10ff", "src": "hda", - "uuid": "a5d093c2-0087-453e-b7d1-d94a7cb664e0" + "uuid": "d402c2ac-ca2d-46b6-b9d3-989739678de1" }, "genbank_files4": { - "id": "0b586e83183b9891", + "id": "8f1ec376bf339086", "src": "hda", - "uuid": "0ec72cc0-2a95-474b-aa77-7a436dad6a9b" + "uuid": "1124ff36-f61b-4932-adc6-0b6de5a888ae" }, "genbank_files5": { - "id": "18d15f79e0c5cee5", + "id": "a91e9fd0ce2e3c53", "src": "hda", - "uuid": "d272199f-2e1b-49e1-a597-5ffa11507e83" + "uuid": "8fe51091-39c5-4aa6-b0ec-fbc34712e405" } }, "job_messages": [], @@ -783,40 +960,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "cf00b67a5455eb5a", + "id": "c32c50a47ebf8564", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "684e8d7e5eb8731e", + "id": "2be24ce9bdbc87e1", "src": "hda", - "uuid": "7435335e-896e-47f4-89c7-3a6c2c25f247" + "uuid": "45ef7ed5-48aa-4286-ac51-3391b593eb7c" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 50.04it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 48.97it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 50.04it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 48.97it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T11:25:33.071688", + "update_time": "2025-05-26T12:04:01.978111", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 3, - "time_seconds": 30.88078260421753, + "time_seconds": 30.717636823654175, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -828,21 +1005,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "8484dc7b019fd65a", + "id": "5493159c7d57114c", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "a3780ecc1a00a0d8", + "id": "5f035ce298b798b0", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/8/e/2/dataset_8e2dcaab-3dd7-48c4-920e-bdffaad39793.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/d/4/2/dataset_d4271a43-8722-4344-9562-00e9a36d07e5.dat,/tmp/tmpc6lic4p9/files/2/4/8/dataset_2484bbfb-d4b0-4c8b-a57f-675625f98753.dat,/tmp/tmpc6lic4p9/files/8/3/f/dataset_83f035f7-25fc-4a59-83b2-d377e3cd59ad.dat,/tmp/tmpc6lic4p9/files/5/a/a/dataset_5aa7b19e-0ad1-43b1-9083-954067ff2010.dat,/tmp/tmpc6lic4p9/files/d/6/4/dataset_d646b71c-5393-4291-bcc5-7d6cbe22f055.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/d/4/2/dataset_d4271a43-8722-4344-9562-00e9a36d07e5.dat:BBa_E0040_GFP.gb,/tmp/tmpc6lic4p9/files/2/4/8/dataset_2484bbfb-d4b0-4c8b-a57f-675625f98753.dat:BBa_J23119_prom.gb,/tmp/tmpc6lic4p9/files/8/3/f/dataset_83f035f7-25fc-4a59-83b2-d377e3cd59ad.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpc6lic4p9/files/5/a/a/dataset_5aa7b19e-0ad1-43b1-9083-954067ff2010.dat:BBa_J61048_term.gb,/tmp/tmpc6lic4p9/files/d/6/4/dataset_d646b71c-5393-4291-bcc5-7d6cbe22f055.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/tmpc6lic4p9/job_working_directory/000/35/outputs/dataset_8086c8c0-24b8-4a51-84db-6b4c9b0e76d0.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/4/9/a/dataset_49af2c08-3ad4-4940-ae84-f93df3c0dd8a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat:BBa_E0040_GFP.gb,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat:BBa_J23119_prom.gb,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat:BBa_J61048_term.gb,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.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/tmpm1fyob3t/job_working_directory/000/35/outputs/dataset_3f72ea64-02f3-413e-9d9a-5c43eaaadf14.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:25:53.885012", + "create_time": "2025-05-26T12:04:23.734013", "dependencies": [ { "cacheable": false, @@ -1022,41 +1199,41 @@ } ], "exit_code": 0, - "external_id": "153816", + "external_id": "174889", "galaxy_version": "24.2", "handler": null, - "history_id": "c7c3cd49f3337c1a", - "id": "684e8d7e5eb8731e", + "history_id": "3937d5ff7c0e1373", + "id": "2be24ce9bdbc87e1", "inputs": { "assembly_csv": { - "id": "8484dc7b019fd65a", + "id": "5493159c7d57114c", "src": "hda", - "uuid": "8e2dcaab-3dd7-48c4-920e-bdffaad39793" + "uuid": "49af2c08-3ad4-4940-ae84-f93df3c0dd8a" }, "genbank_files1": { - "id": "f007b0e97c7852a9", + "id": "8d7d89366ae6734b", "src": "hda", - "uuid": "d4271a43-8722-4344-9562-00e9a36d07e5" + "uuid": "894d0a5e-2d87-4861-85cb-b5cae83b19cb" }, "genbank_files2": { - "id": "0776247cf19fcdeb", + "id": "30133c2583e745a4", "src": "hda", - "uuid": "2484bbfb-d4b0-4c8b-a57f-675625f98753" + "uuid": "315f1808-e9c5-45fb-8cb8-b71e8e1c8366" }, "genbank_files3": { - "id": "428c69cf899eb78e", + "id": "d3fd00b679818750", "src": "hda", - "uuid": "83f035f7-25fc-4a59-83b2-d377e3cd59ad" + "uuid": "b67a6264-6208-4b44-8fd4-47ba3f96faee" }, "genbank_files4": { - "id": "6576e427b69a444e", + "id": "a5593c3e02c9d8f6", "src": "hda", - "uuid": "5aa7b19e-0ad1-43b1-9083-954067ff2010" + "uuid": "ce3a0b5e-0344-4422-b84a-84904818396b" }, "genbank_files5": { - "id": "bd5ff021b11f5160", + "id": "fb42640a8a596816", "src": "hda", - "uuid": "d646b71c-5393-4291-bcc5-7d6cbe22f055" + "uuid": "b7dcace3-2dbd-49db-94ac-98485bf522aa" } }, "job_messages": [], @@ -1067,55 +1244,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "cf75f655bb15877b", + "id": "fbec4a551130f847", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { - "id": "db302e29238adc09", + "id": "f1bdbab1d80457ac", "src": "hda", - "uuid": "d9b71247-a39f-49ea-b279-18a95173730d" + "uuid": "8a7dec58-9e11-4bbf-a945-3910d02c89d9" }, "__new_primary_file_construct_gb|C2_gfp_term__": { - "id": "a0c89ee18eccf84a", + "id": "588795470b41a739", "src": "hda", - "uuid": "cf4710c7-cf67-4f0e-a486-606e525f5689" + "uuid": "ee52fe89-63a0-498c-bdbb-ec9fe5b72eca" }, "__new_primary_file_construct_gb|C3_final__": { - "id": "b326684e3f9ff9a4", + "id": "de619fffe043835f", "src": "hda", - "uuid": "a4ed1a6f-9385-45da-9eda-3fae86d46b5b" + "uuid": "6b8fe4a1-1743-4ec5-a12e-6b7b267efa08" }, "output_zip": { - "id": "e3a5c74dec901fc5", + "id": "a072914da4208f87", "src": "hda", - "uuid": "8086c8c0-24b8-4a51-84db-6b4c9b0e76d0" + "uuid": "3f72ea64-02f3-413e-9d9a-5c43eaaadf14" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:00<00:00, 2.10it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.72it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:00<00:00, 2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.66it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:00<00:00, 2.10it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.72it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:00<00:00, 2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.66it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T11:26:06.650033", + "update_time": "2025-05-26T12:04:36.963198", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 4, - "time_seconds": 33.60218787193298, + "time_seconds": 34.648075580596924, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1127,25 +1304,25 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "ffdd8176dffd877d", + "id": "d61e70858d065388", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "744832bdd7ccd728", + "id": "5bd8560352cb0b69", "src": "hdca" }, "genbank_files": { - "id": "855b83dd0dec8eab", + "id": "cb2fe7fb50f38553", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/9/8/e/dataset_98e1b862-2d3e-4164-aecf-56bd464d0f11.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/b/6/6/dataset_b66afa5b-682d-49f8-9753-c78c356ff228.dat,/tmp/tmpc6lic4p9/files/4/6/e/dataset_46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c.dat,/tmp/tmpc6lic4p9/files/8/3/5/dataset_8358e657-0e61-486b-adb4-e886f0f354ba.dat,/tmp/tmpc6lic4p9/files/4/c/f/dataset_4cfbb2dd-c5a5-42fe-889b-da6510422b72.dat,/tmp/tmpc6lic4p9/files/2/8/c/dataset_28c96444-abfb-4173-970e-e895146aef97.dat,/tmp/tmpc6lic4p9/files/f/5/4/dataset_f54c7a16-ac6f-42c2-9b6c-345af3050d83.dat,/tmp/tmpc6lic4p9/files/2/a/3/dataset_2a330eb7-d033-4e75-be7a-4473748a6f2d.dat' --domesticated_seq '/tmp/tmpc6lic4p9/files/6/8/7/dataset_6877c227-2c70-4080-962e-ee1855dd797f.dat,/tmp/tmpc6lic4p9/files/e/2/1/dataset_e212262c-a336-4263-a076-2cd300590ba4.dat,/tmp/tmpc6lic4p9/files/4/1/1/dataset_4112d545-7e37-4a6e-8ca8-7c1b8f90a71e.dat,/tmp/tmpc6lic4p9/files/b/3/1/dataset_b31955ce-ea44-4e3a-86a1-6aebc47be841.dat,/tmp/tmpc6lic4p9/files/d/4/d/dataset_d4d14388-55d3-4aec-810d-aa902028f29f.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/b/6/6/dataset_b66afa5b-682d-49f8-9753-c78c356ff228.dat:part_A.gb,/tmp/tmpc6lic4p9/files/4/6/e/dataset_46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c.dat:part_B.gb,/tmp/tmpc6lic4p9/files/8/3/5/dataset_8358e657-0e61-486b-adb4-e886f0f354ba.dat:part_C.gb,/tmp/tmpc6lic4p9/files/4/c/f/dataset_4cfbb2dd-c5a5-42fe-889b-da6510422b72.dat:part_D.gb,/tmp/tmpc6lic4p9/files/2/8/c/dataset_28c96444-abfb-4173-970e-e895146aef97.dat:part_E.gb,/tmp/tmpc6lic4p9/files/f/5/4/dataset_f54c7a16-ac6f-42c2-9b6c-345af3050d83.dat:part_F.gb,/tmp/tmpc6lic4p9/files/2/a/3/dataset_2a330eb7-d033-4e75-be7a-4473748a6f2d.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpc6lic4p9/files/6/8/7/dataset_6877c227-2c70-4080-962e-ee1855dd797f.dat:part_H.gb,/tmp/tmpc6lic4p9/files/e/2/1/dataset_e212262c-a336-4263-a076-2cd300590ba4.dat:part_I.gb,/tmp/tmpc6lic4p9/files/4/1/1/dataset_4112d545-7e37-4a6e-8ca8-7c1b8f90a71e.dat:part_J.gb,/tmp/tmpc6lic4p9/files/b/3/1/dataset_b31955ce-ea44-4e3a-86a1-6aebc47be841.dat:part_K.gb,/tmp/tmpc6lic4p9/files/d/4/d/dataset_d4d14388-55d3-4aec-810d-aa902028f29f.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/tmpc6lic4p9/job_working_directory/000/49/outputs/dataset_77f39d12-532c-468b-bcf7-fcc1fdedd34c.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/2/3/dataset_f2390ba6-b891-4c75-b5b4-881fabe15212.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat' --domesticated_seq '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat:part_A.gb,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat:part_B.gb,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat:part_C.gb,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat:part_D.gb,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat:part_E.gb,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat:part_H.gb,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat:part_I.gb,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat:part_J.gb,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat:part_K.gb,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.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/tmpm1fyob3t/job_working_directory/000/49/outputs/dataset_b5c1d918-9a86-47ac-9fd0-0d1eeecb3515.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:26:47.030790", + "create_time": "2025-05-26T12:05:17.468278", "dependencies": [ { "cacheable": false, @@ -1325,76 +1502,76 @@ } ], "exit_code": 0, - "external_id": "154908", + "external_id": "176006", "galaxy_version": "24.2", "handler": null, - "history_id": "51c35891e43131e2", - "id": "0b19a103e85bbfbf", + "history_id": "473b1992d5f5b84f", + "id": "52d2dbb7944a53fc", "inputs": { "assembly_csv": { - "id": "ffdd8176dffd877d", + "id": "d61e70858d065388", "src": "hda", - "uuid": "98e1b862-2d3e-4164-aecf-56bd464d0f11" + "uuid": "f2390ba6-b891-4c75-b5b4-881fabe15212" }, "domesticated_input1": { - "id": "96e47893a0f61173", + "id": "201ce005b4eba284", "src": "hda", - "uuid": "6877c227-2c70-4080-962e-ee1855dd797f" + "uuid": "b263e11f-1d52-45d4-8679-8bb23668154a" }, "domesticated_input2": { - "id": "07b1a06cea2f6611", + "id": "ccacdf94e033958e", "src": "hda", - "uuid": "e212262c-a336-4263-a076-2cd300590ba4" + "uuid": "c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee" }, "domesticated_input3": { - "id": "7c42ebb9622f8a60", + "id": "71f633fb8d250097", "src": "hda", - "uuid": "4112d545-7e37-4a6e-8ca8-7c1b8f90a71e" + "uuid": "ddcb9f93-9b4f-41e3-a1df-5537b6326a78" }, "domesticated_input4": { - "id": "33456f383510d381", + "id": "23971c9dcf22198b", "src": "hda", - "uuid": "b31955ce-ea44-4e3a-86a1-6aebc47be841" + "uuid": "99bac98d-1cbf-4ab1-a680-49cdb721e447" }, "domesticated_input5": { - "id": "3c2a17e7ec6c065d", + "id": "60438d790668bc40", "src": "hda", - "uuid": "d4d14388-55d3-4aec-810d-aa902028f29f" + "uuid": "685cd571-80b5-4c03-b247-4fb51e199639" }, "genbank_files1": { - "id": "c2ddc784389f17d2", + "id": "562cdacb0f854350", "src": "hda", - "uuid": "b66afa5b-682d-49f8-9753-c78c356ff228" + "uuid": "dfe71b71-2603-48cf-bf59-772724abea0f" }, "genbank_files2": { - "id": "79b5ff6df7bc6716", + "id": "b5f666ac47f1f830", "src": "hda", - "uuid": "46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c" + "uuid": "09260017-ac9e-4868-b386-27ef07ca03a8" }, "genbank_files3": { - "id": "6f172ec7c3220722", + "id": "316b2bf479d3691f", "src": "hda", - "uuid": "8358e657-0e61-486b-adb4-e886f0f354ba" + "uuid": "84e57026-4e85-4a63-b66a-8bae5b767f0c" }, "genbank_files4": { - "id": "0b19a103e85bbfbf", + "id": "52d2dbb7944a53fc", "src": "hda", - "uuid": "4cfbb2dd-c5a5-42fe-889b-da6510422b72" + "uuid": "7d26d36d-bb1c-4f83-be4f-3311e4ec2441" }, "genbank_files5": { - "id": "00fa99289b8a441d", + "id": "6d0420a098f813ba", "src": "hda", - "uuid": "28c96444-abfb-4173-970e-e895146aef97" + "uuid": "8a0ff1e5-aaf7-461e-b642-b60e5cf13132" }, "genbank_files6": { - "id": "95a08e54dcf8e4b4", + "id": "98086fd4fda4fb74", "src": "hda", - "uuid": "f54c7a16-ac6f-42c2-9b6c-345af3050d83" + "uuid": "f94fb7c9-761b-4dc1-8caa-a02ee7892c59" }, "genbank_files7": { - "id": "46fceb9ab6cb9139", + "id": "1e3f8509b9833e4e", "src": "hda", - "uuid": "2a330eb7-d033-4e75-be7a-4473748a6f2d" + "uuid": "c7e408b5-927b-4966-8d1f-08de3b41fc34" } }, "job_messages": [], @@ -1405,60 +1582,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "c173cff58a987f8f", + "id": "1e8e6749bc68d8e8", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "887639ccacb877d4", + "id": "825e5e92a55932c1", "src": "hda", - "uuid": "ac0f5082-55fc-4fb6-b3ef-f2587cdd2662" + "uuid": "fd97fd7a-08b9-42ba-ae2a-022c8be1b219" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "97c509c62c06ea77", + "id": "4a8ace5529c8c3e9", "src": "hda", - "uuid": "9e439105-9563-450d-96a3-bec58242389e" + "uuid": "b9201d86-ee66-45ac-99a5-09d3ca161d8b" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "05372c5ab71bbd4d", + "id": "f0d76a7bda3035c9", "src": "hda", - "uuid": "13079e9f-8185-4b43-898a-83348a3fe55b" + "uuid": "7c74cbab-8a62-43a2-95f3-00919cc11fa7" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "14e667eccbf3c9ac", + "id": "640790f555d03105", "src": "hda", - "uuid": "4aec2395-19a8-49b5-a927-39b5b06dabe7" + "uuid": "a450e128-38e8-4eb5-82a1-304b04c68510" }, "output_zip": { - "id": "edb47c5501e52d48", + "id": "50943f113f3eedaf", "src": "hda", - "uuid": "77f39d12-532c-468b-bcf7-fcc1fdedd34c" + "uuid": "b5c1d918-9a86-47ac-9fd0-0d1eeecb3515" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.31it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.14it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.74it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.40it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.31it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.14it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.74it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.40it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T11:27:00.365017", + "update_time": "2025-05-26T12:05:29.989306", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 5, - "time_seconds": 53.75153422355652, + "time_seconds": 53.09692740440369, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1470,21 +1647,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "59a0a00f5fa501d5", + "id": "d71403ee85b47d8d", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "c9445e550eef23d0", + "id": "a36db940f4513bd9", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/9/5/0/dataset_9504897d-0d99-44a4-9033-7d14e3943ec9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/a/c/d/dataset_acd9e546-bb31-4391-b867-1d81cab10920.dat,/tmp/tmpc6lic4p9/files/c/f/e/dataset_cfe852f6-5b32-46fd-a9d8-2b777016d403.dat,/tmp/tmpc6lic4p9/files/2/5/b/dataset_25be2770-f768-4b0e-be96-459e47e6ae8d.dat,/tmp/tmpc6lic4p9/files/e/5/8/dataset_e580f806-e8ba-4dac-b8d5-6b76b4a7421b.dat,/tmp/tmpc6lic4p9/files/0/d/6/dataset_0d6de31a-aab1-427f-a2a1-7c8bc988208e.dat,/tmp/tmpc6lic4p9/files/1/2/7/dataset_1272b23f-7cef-4deb-bf92-fbad973bf2c6.dat,/tmp/tmpc6lic4p9/files/7/4/7/dataset_7476b10d-c143-4be7-adb5-118dcf372287.dat,/tmp/tmpc6lic4p9/files/e/2/e/dataset_e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a.dat,/tmp/tmpc6lic4p9/files/c/a/1/dataset_ca18b50c-3b4c-4201-88b0-dffd049718f8.dat,/tmp/tmpc6lic4p9/files/1/b/4/dataset_1b480e84-03cf-4483-9e9e-ccf79bf654a1.dat,/tmp/tmpc6lic4p9/files/b/e/8/dataset_be83b8f4-73de-4775-abb8-75483d4e8ab2.dat,/tmp/tmpc6lic4p9/files/5/d/d/dataset_5ddde548-4828-4067-93b7-1377a71221d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/a/c/d/dataset_acd9e546-bb31-4391-b867-1d81cab10920.dat:part_A.gb,/tmp/tmpc6lic4p9/files/c/f/e/dataset_cfe852f6-5b32-46fd-a9d8-2b777016d403.dat:part_B.gb,/tmp/tmpc6lic4p9/files/2/5/b/dataset_25be2770-f768-4b0e-be96-459e47e6ae8d.dat:part_C.gb,/tmp/tmpc6lic4p9/files/e/5/8/dataset_e580f806-e8ba-4dac-b8d5-6b76b4a7421b.dat:part_D.gb,/tmp/tmpc6lic4p9/files/0/d/6/dataset_0d6de31a-aab1-427f-a2a1-7c8bc988208e.dat:part_E.gb,/tmp/tmpc6lic4p9/files/1/2/7/dataset_1272b23f-7cef-4deb-bf92-fbad973bf2c6.dat:part_F.gb,/tmp/tmpc6lic4p9/files/7/4/7/dataset_7476b10d-c143-4be7-adb5-118dcf372287.dat:part_G.gb,/tmp/tmpc6lic4p9/files/e/2/e/dataset_e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a.dat:part_H.gb,/tmp/tmpc6lic4p9/files/c/a/1/dataset_ca18b50c-3b4c-4201-88b0-dffd049718f8.dat:part_I.gb,/tmp/tmpc6lic4p9/files/1/b/4/dataset_1b480e84-03cf-4483-9e9e-ccf79bf654a1.dat:part_J.gb,/tmp/tmpc6lic4p9/files/b/e/8/dataset_be83b8f4-73de-4775-abb8-75483d4e8ab2.dat:part_K.gb,/tmp/tmpc6lic4p9/files/5/d/d/dataset_5ddde548-4828-4067-93b7-1377a71221d7.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/tmpc6lic4p9/job_working_directory/000/63/outputs/dataset_e10784a6-3050-4131-a684-3847397c4c4d.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/3/c/1/dataset_3c1221bc-ba53-4ede-899c-e4defbe838eb.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat:part_A.gb,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat:part_B.gb,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat:part_C.gb,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat:part_D.gb,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat:part_E.gb,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat:part_F.gb,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat:part_G.gb,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat:part_H.gb,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat:part_I.gb,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat:part_J.gb,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat:part_K.gb,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.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/tmpm1fyob3t/job_working_directory/000/63/outputs/dataset_02e7ea5e-6c8f-419d-82de-476bccc550ec.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T11:27:41.184534", + "create_time": "2025-05-26T12:06:09.749817", "dependencies": [ { "cacheable": false, @@ -1664,76 +1841,76 @@ } ], "exit_code": 0, - "external_id": "155964", + "external_id": "177047", "galaxy_version": "24.2", "handler": null, - "history_id": "84db48b219855f4d", - "id": "14e667eccbf3c9ac", + "history_id": "9b5c1fe7a52a75e0", + "id": "640790f555d03105", "inputs": { "assembly_csv": { - "id": "59a0a00f5fa501d5", + "id": "d71403ee85b47d8d", "src": "hda", - "uuid": "9504897d-0d99-44a4-9033-7d14e3943ec9" + "uuid": "3c1221bc-ba53-4ede-899c-e4defbe838eb" }, "domesticated_input1": { - "id": "2252f6534dc04be9", + "id": "740094ed962e7335", "src": "hda", - "uuid": "acd9e546-bb31-4391-b867-1d81cab10920" + "uuid": "68ee2e69-c2d9-43cd-851e-0b660884cac2" }, "domesticated_input10": { - "id": "b26f1eae65161bae", + "id": "06981e06b6149081", "src": "hda", - "uuid": "1b480e84-03cf-4483-9e9e-ccf79bf654a1" + "uuid": "04bcf9c1-ccc8-4d52-a739-fb3630f90b05" }, "domesticated_input11": { - "id": "748ef145f2d110fe", + "id": "343d33e0d7549cb9", "src": "hda", - "uuid": "be83b8f4-73de-4775-abb8-75483d4e8ab2" + "uuid": "402aaabe-0ea9-4519-998b-11cf6b07a1df" }, "domesticated_input12": { - "id": "37a05bd56b325e88", + "id": "2c330e522704b0f9", "src": "hda", - "uuid": "5ddde548-4828-4067-93b7-1377a71221d7" + "uuid": "9cf71985-a62d-4d89-845c-2b996d8096fa" }, "domesticated_input2": { - "id": "2441550d408330ea", + "id": "839c90adaefe5f3f", "src": "hda", - "uuid": "cfe852f6-5b32-46fd-a9d8-2b777016d403" + "uuid": "5c298af3-9cdb-4837-8054-8903c2683f85" }, "domesticated_input3": { - "id": "7982f5ab86225272", + "id": "1f56aa824e7dde43", "src": "hda", - "uuid": "25be2770-f768-4b0e-be96-459e47e6ae8d" + "uuid": "9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e" }, "domesticated_input4": { - "id": "1d0be35bf9fc6600", + "id": "26b32a65097dcc1d", "src": "hda", - "uuid": "e580f806-e8ba-4dac-b8d5-6b76b4a7421b" + "uuid": "e77c955d-e9b5-4175-a061-81b9a781d2ff" }, "domesticated_input5": { - "id": "40fe86a604adcf6d", + "id": "60327bfb8991788f", "src": "hda", - "uuid": "0d6de31a-aab1-427f-a2a1-7c8bc988208e" + "uuid": "35df1ceb-416b-4c2d-b20a-3efe96b6770f" }, "domesticated_input6": { - "id": "7355915c318fd136", + "id": "ac528058169ea450", "src": "hda", - "uuid": "1272b23f-7cef-4deb-bf92-fbad973bf2c6" + "uuid": "c02fc9fb-dc4e-49e1-b99f-8199fd97d795" }, "domesticated_input7": { - "id": "bacbde4487432826", + "id": "8d7c8aec2b1ab229", "src": "hda", - "uuid": "7476b10d-c143-4be7-adb5-118dcf372287" + "uuid": "339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a" }, "domesticated_input8": { - "id": "3b9b440d32d1c6f3", + "id": "f996cb18f164a451", "src": "hda", - "uuid": "e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a" + "uuid": "2246947a-dbb7-4ed2-855a-56a42a899aab" }, "domesticated_input9": { - "id": "a19ae27f3bb8e8c1", + "id": "f3c4f2ef486441ac", "src": "hda", - "uuid": "ca18b50c-3b4c-4201-88b0-dffd049718f8" + "uuid": "0a935c03-48a7-4c8a-8077-aea407e5285d" } }, "job_messages": [], @@ -1744,60 +1921,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "fedb85639c7c80b9", + "id": "182eefa577c2a56d", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "94b6b8378debd859", + "id": "613a1bff017ef479", "src": "hda", - "uuid": "5145585f-443e-4934-af0b-60e1552a08a9" + "uuid": "a0c57d2e-8ac7-48d8-b9c5-f01b728ebba7" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "dfa4bbdeadf76cd3", + "id": "1a8ab2437d7e496f", "src": "hda", - "uuid": "6f0dcaec-2131-4c0c-820b-bb5c895103e2" + "uuid": "d7804ee2-c9a8-46c2-b057-7f25a8002f55" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "e48032fd92b02fbb", + "id": "af3c5f81417a677c", "src": "hda", - "uuid": "8c4da7fd-9c6b-4430-9444-c6e89b41c5df" + "uuid": "71c1f25b-f43d-43f7-9893-bfd3bc967517" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "68bf450f38f03a28", + "id": "b5b1a9766aab456e", "src": "hda", - "uuid": "a878e0a8-6f34-4cdf-8990-e178d0f15d52" + "uuid": "f23f1069-e4c4-4a9e-9787-5b2b5e905e24" }, "output_zip": { - "id": "1062de4bcda0d565", + "id": "7d40cd3e06526c58", "src": "hda", - "uuid": "e10784a6-3050-4131-a684-3847397c4c4d" + "uuid": "02e7ea5e-6c8f-419d-82de-476bccc550ec" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", "genbank_files": null, "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.45it/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", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.45it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T11:27:53.929264", + "update_time": "2025-05-26T12:06:22.164674", "user_email": "planemo@galaxyproject.org", - "user_id": "fcc5b7d13a1328f6" + "user_id": "e2ca7f14a85a8d44" }, "status": "success", "test_index": 6, - "time_seconds": 53.42731332778931, + "time_seconds": 52.117783308029175, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" },