Mercurial > repos > tduigou > cloning_simulation
diff output.json @ 10:0be569bd5443 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 09:50:30 +0000 |
| parents | 07e902da89ad |
| children | 7d1778f5e164 |
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--- a/output.json Mon May 26 09:43:40 2025 +0000 +++ b/output.json Mon May 26 09:50:30 2025 +0000 @@ -11,93 +11,93 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "0a696a8b22798e06", + "id": "7a37f3397bf88665", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { - "id": "cb6d3fbb91be6861", + "id": "b5f519d254c4f536", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/b/a/a/dataset_baa59b14-7fb5-4efc-a75d-228d26b70adc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/14/outputs/dataset_49164d85-9bff-47f5-b8ee-de001d155fd3.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/6/1/a/dataset_61aa4b8a-d71a-4e9d-a878-5f0d1494b36d.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/f/c/e/dataset_fce5b5a1-92e2-4c39-90d5-0eddf56635f0.dat,/tmp/tmphxxoceah/files/a/6/4/dataset_a6400a83-e4fd-488b-94e8-5ec1f44db9ca.dat,/tmp/tmphxxoceah/files/a/6/6/dataset_a66c7ac9-f828-405d-9a49-842e978b00af.dat,/tmp/tmphxxoceah/files/5/4/b/dataset_54b878ab-05e6-4212-b399-ab1f62c59e16.dat,/tmp/tmphxxoceah/files/3/9/0/dataset_39021efe-6a4f-4b7f-ba0d-f87c2b436a0f.dat,/tmp/tmphxxoceah/files/b/e/2/dataset_be26c9ab-28e8-449a-bd01-2047af0dfa5d.dat,/tmp/tmphxxoceah/files/f/7/f/dataset_f7fd1975-81bc-4a4f-89c6-d946d59782ee.dat,/tmp/tmphxxoceah/files/f/b/1/dataset_fb1f0888-2487-4f14-bcdd-fa06923d4cd9.dat,/tmp/tmphxxoceah/files/2/5/0/dataset_250500a7-25ca-4cba-8d71-7d16053afcaa.dat,/tmp/tmphxxoceah/files/3/8/7/dataset_387ad7a6-1931-4a46-99d5-4513ba93a999.dat,/tmp/tmphxxoceah/files/6/8/2/dataset_6829a587-673a-44a6-8bcf-ec6334a9184f.dat,/tmp/tmphxxoceah/files/4/0/4/dataset_40405cee-d70a-45d6-ac91-05616fe798b9.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/f/c/e/dataset_fce5b5a1-92e2-4c39-90d5-0eddf56635f0.dat:part_A.gb,/tmp/tmphxxoceah/files/a/6/4/dataset_a6400a83-e4fd-488b-94e8-5ec1f44db9ca.dat:part_B.gb,/tmp/tmphxxoceah/files/a/6/6/dataset_a66c7ac9-f828-405d-9a49-842e978b00af.dat:part_C.gb,/tmp/tmphxxoceah/files/5/4/b/dataset_54b878ab-05e6-4212-b399-ab1f62c59e16.dat:part_D.gb,/tmp/tmphxxoceah/files/3/9/0/dataset_39021efe-6a4f-4b7f-ba0d-f87c2b436a0f.dat:part_E.gb,/tmp/tmphxxoceah/files/b/e/2/dataset_be26c9ab-28e8-449a-bd01-2047af0dfa5d.dat:part_F.gb,/tmp/tmphxxoceah/files/f/7/f/dataset_f7fd1975-81bc-4a4f-89c6-d946d59782ee.dat:part_G.gb,/tmp/tmphxxoceah/files/f/b/1/dataset_fb1f0888-2487-4f14-bcdd-fa06923d4cd9.dat:part_H.gb,/tmp/tmphxxoceah/files/2/5/0/dataset_250500a7-25ca-4cba-8d71-7d16053afcaa.dat:part_I.gb,/tmp/tmphxxoceah/files/3/8/7/dataset_387ad7a6-1931-4a46-99d5-4513ba93a999.dat:part_J.gb,/tmp/tmphxxoceah/files/6/8/2/dataset_6829a587-673a-44a6-8bcf-ec6334a9184f.dat:part_K.gb,/tmp/tmphxxoceah/files/4/0/4/dataset_40405cee-d70a-45d6-ac91-05616fe798b9.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/tmphxxoceah/job_working_directory/000/14/outputs/dataset_a840b0de-7374-4fc2-bc9c-eec0f6615e2f.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:56:03.115650", + "create_time": "2025-05-26T09:44:56.264493", "dependencies": [], "exit_code": 0, - "external_id": "78665", + "external_id": "102136", "galaxy_version": "24.2", "handler": null, - "history_id": "cb6d3fbb91be6861", - "id": "2ff5b0f6b4cfbb73", + "history_id": "b5f519d254c4f536", + "id": "dfd75d2f0da631b2", "inputs": { "assembly_csv": { - "id": "0a696a8b22798e06", + "id": "7a37f3397bf88665", "src": "hda", - "uuid": "baa59b14-7fb5-4efc-a75d-228d26b70adc" + "uuid": "61aa4b8a-d71a-4e9d-a878-5f0d1494b36d" }, "genbank_files1": { - "id": "cb6d3fbb91be6861", + "id": "b5f519d254c4f536", "src": "hda", - "uuid": "f7bde375-2c6b-4e23-9117-e96bb4c3f6e6" + "uuid": "fce5b5a1-92e2-4c39-90d5-0eddf56635f0" }, "genbank_files10": { - "id": "7ede2556a40dc9ba", + "id": "2bdc7fcb2931f07b", "src": "hda", - "uuid": "3217492e-bc97-4d61-87fd-b9d1f2e4534d" + "uuid": "387ad7a6-1931-4a46-99d5-4513ba93a999" }, "genbank_files11": { - "id": "76608081d307dc20", + "id": "dc7e3ab6a421767b", "src": "hda", - "uuid": "f8f04302-598c-4596-99a1-6c7d84b613d6" + "uuid": "6829a587-673a-44a6-8bcf-ec6334a9184f" }, "genbank_files12": { - "id": "0551bf01e3dbca02", + "id": "b1d9a1d43e36b679", "src": "hda", - "uuid": "9f67cbfd-ca06-4926-b042-74a0d43b585a" + "uuid": "40405cee-d70a-45d6-ac91-05616fe798b9" }, "genbank_files2": { - "id": "18a1e53d7b8ec0fa", + "id": "c5accd210dc5c9dd", "src": "hda", - "uuid": "ba5c9d10-e47e-4ced-9aaf-a51bf18e7932" + "uuid": "a6400a83-e4fd-488b-94e8-5ec1f44db9ca" }, "genbank_files3": { - "id": "afdf3d24f0e34eea", + "id": "10fbf206fb2087c4", "src": "hda", - "uuid": "bf6e6482-afaa-4790-ac74-23f532fa48ad" + "uuid": "a66c7ac9-f828-405d-9a49-842e978b00af" }, "genbank_files4": { - "id": "285751a21c9d1d68", + "id": "27fa0815bff520f2", "src": "hda", - "uuid": "1b8c7b47-fdba-4046-953a-89dc0c07ae14" + "uuid": "54b878ab-05e6-4212-b399-ab1f62c59e16" }, "genbank_files5": { - "id": "48e4779cf88cf124", + "id": "f825d543d1b9cf39", "src": "hda", - "uuid": "5f5321b9-fa9a-4a73-9573-890d0c00209d" + "uuid": "39021efe-6a4f-4b7f-ba0d-f87c2b436a0f" }, "genbank_files6": { - "id": "2bf3ecab9316a382", + "id": "24f234959abeadac", "src": "hda", - "uuid": "8557a762-7c36-4111-a015-2b61caad4e5b" + "uuid": "be26c9ab-28e8-449a-bd01-2047af0dfa5d" }, "genbank_files7": { - "id": "d51bf47fbc922335", + "id": "67e443cb5516c0e0", "src": "hda", - "uuid": "f7000fc2-7e04-4561-875c-b84614f51966" + "uuid": "f7fd1975-81bc-4a4f-89c6-d946d59782ee" }, "genbank_files8": { - "id": "590bb56cc83504dc", + "id": "5180b1a726879d60", "src": "hda", - "uuid": "3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09" + "uuid": "fb1f0888-2487-4f14-bcdd-fa06923d4cd9" }, "genbank_files9": { - "id": "ff96e44e65db99f8", + "id": "c3b441e1ed1e9870", "src": "hda", - "uuid": "e3b26d77-5d05-4a0f-adf7-016bf86c5eb3" + "uuid": "250500a7-25ca-4cba-8d71-7d16053afcaa" } }, "job_messages": [], @@ -108,60 +108,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "18a1e53d7b8ec0fa", + "id": "c5accd210dc5c9dd", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "be5466d8eb2c2229", + "id": "cecf675ce2a554e8", "src": "hda", - "uuid": "2c83aaa9-63df-43a5-b008-9a361a9fc312" + "uuid": "3f70ca65-7fb8-4f83-b6e7-3f9893b1db5e" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "a37f81f30817f4ff", + "id": "9cc1fc667f1eccc7", "src": "hda", - "uuid": "8ba2ce56-ba8b-4ff8-bcc0-54d0a2ad3b09" + "uuid": "723df0ab-a674-4b94-b805-15e38f56cbd5" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "b4705f371a43addc", + "id": "0b28ef6dfa05b9a4", "src": "hda", - "uuid": "47741e71-6bf6-46ec-9353-25bb48d895ed" + "uuid": "0225d884-89af-4b29-bf0c-d27e776614a3" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "0dc911fcb05967a3", + "id": "dd0a4ddfadd2b33c", "src": "hda", - "uuid": "6aa740ec-6985-4d66-8427-b1652fa06f3a" + "uuid": "2495d80c-1c1d-4aa7-af8c-eac0dd199af2" }, "output_zip": { - "id": "2ff5b0f6b4cfbb73", + "id": "dfd75d2f0da631b2", "src": "hda", - "uuid": "49164d85-9bff-47f5-b8ee-de001d155fd3" + "uuid": "a840b0de-7374-4fc2-bc9c-eec0f6615e2f" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.83it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/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, 1.83it/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": "2025-05-26T08:56:15.534051", + "update_time": "2025-05-26T09:45:09.253153", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 0, - "time_seconds": 54.95904994010925, + "time_seconds": 53.940672636032104, "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": "e01f0df21d75058c", + "id": "191f29e52861c771", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { - "id": "afdf3d24f0e34eea", + "id": "10fbf206fb2087c4", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/b/2/dataset_5b2e01d9-e63b-45e1-8523-e88570aecbd1.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/17/outputs/dataset_81c8307a-8e03-4975-b3ec-1115f4f47284.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/a/e/1/dataset_ae19b93d-96dc-4575-922e-1c1b13cdda00.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/6/6/b/dataset_66becc5b-d90e-4bca-8456-82d9f7c209ea.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/6/6/b/dataset_66becc5b-d90e-4bca-8456-82d9f7c209ea.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/tmphxxoceah/job_working_directory/000/17/outputs/dataset_cf3ea990-c609-45fe-a823-8786fed863f9.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:56:26.250368", + "create_time": "2025-05-26T09:45:19.833949", "dependencies": [ { "cacheable": false, @@ -367,21 +367,21 @@ } ], "exit_code": 0, - "external_id": "79009", + "external_id": "102481", "galaxy_version": "24.2", "handler": null, - "history_id": "18a1e53d7b8ec0fa", - "id": "b4705f371a43addc", + "history_id": "c5accd210dc5c9dd", + "id": "0b28ef6dfa05b9a4", "inputs": { "assembly_csv": { - "id": "e01f0df21d75058c", + "id": "191f29e52861c771", "src": "hda", - "uuid": "5b2e01d9-e63b-45e1-8523-e88570aecbd1" + "uuid": "ae19b93d-96dc-4575-922e-1c1b13cdda00" }, "genbank_files1": { - "id": "bc8da7662961ae94", + "id": "1bd551c439d3389f", "src": "hda", - "uuid": "5633084d-0123-48ba-b733-086550a95944" + "uuid": "66becc5b-d90e-4bca-8456-82d9f7c209ea" } }, "job_messages": [], @@ -392,55 +392,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "285751a21c9d1d68", + "id": "27fa0815bff520f2", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "d8c348e4a6c18790", + "id": "a74d82facdf691d6", "src": "hda", - "uuid": "39e12d2a-e4aa-491e-bb74-be0d48efaa36" + "uuid": "d06a3b4e-424a-4af4-b067-8426c2170c90" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "cc98bdb1867cbf6a", + "id": "7d2e9c5805bbd6ea", "src": "hda", - "uuid": "dbc568c1-dd73-4973-aa7a-f33cb279cbb7" + "uuid": "1f95f8b0-5fc6-4b06-9550-06dd8233e6bd" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "dd60b22cea40a264", + "id": "6c4aee794b3972b4", "src": "hda", - "uuid": "3d0514f2-d798-484f-add3-d04103fef517" + "uuid": "cfd50000-e85e-4b17-985e-f137dc59b08b" }, "output_zip": { - "id": "cb5bc2d1019b090c", + "id": "e670fc59d69da207", "src": "hda", - "uuid": "81c8307a-8e03-4975-b3ec-1115f4f47284" + "uuid": "cf3ea990-c609-45fe-a823-8786fed863f9" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"GibsonAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/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, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/s, now=None]\r \r", + "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, 4.34it/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, 3.56it/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, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/s, now=None]\r \r", + "tool_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, 4.34it/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, 3.56it/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": "2025-05-26T08:56:38.283009", + "update_time": "2025-05-26T09:45:31.869394", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 1, - "time_seconds": 22.636474609375, + "time_seconds": 22.247495412826538, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -452,21 +452,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "c6996082322986ef", + "id": "83c94260ae237f16", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { - "id": "48e4779cf88cf124", + "id": "f825d543d1b9cf39", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/3/6/c/dataset_36c9642c-c980-4a5f-babe-e1140450965b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/21/outputs/dataset_dd39a396-84ad-4350-8d9b-a0efafd5ea2a.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/8/2/c/dataset_82c2d90b-0ca3-4633-915b-eaa0ab81b80f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/c/b/f/dataset_cbf24487-bf9d-469a-99cd-bccebb2bc139.dat,/tmp/tmphxxoceah/files/d/3/d/dataset_d3d42e4b-1982-4660-8ad4-f12c8a0599cb.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/c/b/f/dataset_cbf24487-bf9d-469a-99cd-bccebb2bc139.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmphxxoceah/files/d/3/d/dataset_d3d42e4b-1982-4660-8ad4-f12c8a0599cb.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/tmphxxoceah/job_working_directory/000/21/outputs/dataset_233ed98e-ee9b-468f-8145-9a8c44e8034f.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:56:49.662294", + "create_time": "2025-05-26T09:45:42.951843", "dependencies": [ { "cacheable": false, @@ -646,26 +646,26 @@ } ], "exit_code": 0, - "external_id": "79436", + "external_id": "102861", "galaxy_version": "24.2", "handler": null, - "history_id": "afdf3d24f0e34eea", - "id": "cb5bc2d1019b090c", + "history_id": "10fbf206fb2087c4", + "id": "e670fc59d69da207", "inputs": { "assembly_csv": { - "id": "c6996082322986ef", + "id": "83c94260ae237f16", "src": "hda", - "uuid": "36c9642c-c980-4a5f-babe-e1140450965b" + "uuid": "82c2d90b-0ca3-4633-915b-eaa0ab81b80f" }, "genbank_files1": { - "id": "ff6721ae641686bd", + "id": "57b57ab024b6e67d", "src": "hda", - "uuid": "fd7feec8-d839-4aac-ba59-54d4042d72d4" + "uuid": "cbf24487-bf9d-469a-99cd-bccebb2bc139" }, "genbank_files2": { - "id": "898f771988549b05", + "id": "71d78516c0fe784e", "src": "hda", - "uuid": "097d3af5-48d7-4b15-9063-19cc11585d82" + "uuid": "d3d42e4b-1982-4660-8ad4-f12c8a0599cb" } }, "job_messages": [], @@ -676,40 +676,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "2bf3ecab9316a382", + "id": "24f234959abeadac", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "b995dfb8c32b92b7", + "id": "1211f83788e0a9a2", "src": "hda", - "uuid": "dd39a396-84ad-4350-8d9b-a0efafd5ea2a" + "uuid": "233ed98e-ee9b-468f-8145-9a8c44e8034f" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/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, 2.23it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.38it/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, 2.23it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.38it/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": "2025-05-26T08:57:02.321903", + "update_time": "2025-05-26T09:45:54.473182", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 2, - "time_seconds": 23.856895685195923, + "time_seconds": 22.476279258728027, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -721,21 +721,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "9d9573fdc2182066", + "id": "2aab5679a1ae5c57", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { - "id": "d51bf47fbc922335", + "id": "67e443cb5516c0e0", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/2/5/1/dataset_251d413f-0fe8-42cd-8a76-7ef77cde6f15.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat:GFP.gb,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat:p15A_kan.gb,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat:promoter.gb,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat:RFP.gb,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/28/outputs/dataset_8e6b31eb-84b3-4184-92eb-33384ae50857.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/2/c/3/dataset_2c3186df-93d9-4d24-8956-c6a17e7d822a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/1/d/8/dataset_1d824d9e-0b4f-4a81-af49-1acb506e8f4b.dat,/tmp/tmphxxoceah/files/5/7/d/dataset_57d780ae-3783-4cdf-a295-642ebc88a60e.dat,/tmp/tmphxxoceah/files/b/8/9/dataset_b89b536e-e310-470d-bddc-cd2847c2cfff.dat,/tmp/tmphxxoceah/files/b/b/d/dataset_bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8.dat,/tmp/tmphxxoceah/files/0/6/5/dataset_06587a95-951c-4c6f-bded-3df9fd38a5d1.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/1/d/8/dataset_1d824d9e-0b4f-4a81-af49-1acb506e8f4b.dat:GFP.gb,/tmp/tmphxxoceah/files/5/7/d/dataset_57d780ae-3783-4cdf-a295-642ebc88a60e.dat:p15A_kan.gb,/tmp/tmphxxoceah/files/b/8/9/dataset_b89b536e-e310-470d-bddc-cd2847c2cfff.dat:promoter.gb,/tmp/tmphxxoceah/files/b/b/d/dataset_bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8.dat:RFP.gb,/tmp/tmphxxoceah/files/0/6/5/dataset_06587a95-951c-4c6f-bded-3df9fd38a5d1.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/tmphxxoceah/job_working_directory/000/28/outputs/dataset_003ab152-a58f-45ab-a3c5-38a87199b77d.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:57:24.342653", + "create_time": "2025-05-26T09:46:15.589461", "dependencies": [ { "cacheable": false, @@ -915,41 +915,41 @@ } ], "exit_code": 0, - "external_id": "80040", + "external_id": "103494", "galaxy_version": "24.2", "handler": null, - "history_id": "285751a21c9d1d68", - "id": "b995dfb8c32b92b7", + "history_id": "27fa0815bff520f2", + "id": "1211f83788e0a9a2", "inputs": { "assembly_csv": { - "id": "9d9573fdc2182066", + "id": "2aab5679a1ae5c57", "src": "hda", - "uuid": "251d413f-0fe8-42cd-8a76-7ef77cde6f15" + "uuid": "2c3186df-93d9-4d24-8956-c6a17e7d822a" }, "genbank_files1": { - "id": "241cfac882733d83", + "id": "0164abbd74b9b05d", "src": "hda", - "uuid": "7d893bbf-b4e0-4d64-bafc-21ba1566237d" + "uuid": "1d824d9e-0b4f-4a81-af49-1acb506e8f4b" }, "genbank_files2": { - "id": "7ada2c781708b1e8", + "id": "f5f5feeed891820d", "src": "hda", - "uuid": "cc2314fa-924f-47c0-b89a-661fb78790a4" + "uuid": "57d780ae-3783-4cdf-a295-642ebc88a60e" }, "genbank_files3": { - "id": "4deb8a541e3f0671", + "id": "b3161e3b65353042", "src": "hda", - "uuid": "8d097c97-7bd5-48eb-9f9e-f5b92ce19458" + "uuid": "b89b536e-e310-470d-bddc-cd2847c2cfff" }, "genbank_files4": { - "id": "cdcc9004d7157de8", + "id": "292aa45e4e016cce", "src": "hda", - "uuid": "59189305-e832-4191-be7c-496c01c8aba6" + "uuid": "bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8" }, "genbank_files5": { - "id": "33fad5084f4d4cb5", + "id": "9318ef3621fbfa11", "src": "hda", - "uuid": "402500d7-6532-4008-9445-c0cf7fed5350" + "uuid": "06587a95-951c-4c6f-bded-3df9fd38a5d1" } }, "job_messages": [], @@ -960,40 +960,40 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "590bb56cc83504dc", + "id": "5180b1a726879d60", "src": "hdca" } }, "outputs": { "output_zip": { - "id": "4f510c4214d7d568", + "id": "4b5a70f26b4819b4", "src": "hda", - "uuid": "8e6b31eb-84b3-4184-92eb-33384ae50857" + "uuid": "003ab152-a58f-45ab-a3c5-38a87199b77d" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BASICAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/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, 49.38it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.32it/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, 49.38it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.32it/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": "2025-05-26T08:57:34.740635", + "update_time": "2025-05-26T09:46:26.255886", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 3, - "time_seconds": 32.283992767333984, + "time_seconds": 31.84161639213562, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1005,21 +1005,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "017df84d4155fcba", + "id": "6aba8bde83c91d2f", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { - "id": "ff96e44e65db99f8", + "id": "c3b441e1ed1e9870", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/f/d/9/dataset_fd913c0f-ea98-4b8d-a170-961146c201d5.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat:BBa_E0040_GFP.gb,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat:BBa_J23119_prom.gb,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat:BBa_J23119_prom_flawed.gb,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat:BBa_J61048_term.gb,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/35/outputs/dataset_a3f2eab1-bbe1-401e-b436-b7ffc698ee3a.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/2/a/d/dataset_2ad0d873-86c6-45d9-b7d2-124dcbc1af89.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/d/2/9/dataset_d293bdbb-5524-4e82-a4a0-d687a407a968.dat,/tmp/tmphxxoceah/files/e/a/5/dataset_ea5e46a6-144f-4c5e-b626-6bca5055f710.dat,/tmp/tmphxxoceah/files/b/4/9/dataset_b491036e-78aa-4140-bca6-63462b7dbb5a.dat,/tmp/tmphxxoceah/files/1/c/f/dataset_1cf514a1-2062-47c1-98b3-d86c408d348d.dat,/tmp/tmphxxoceah/files/d/0/a/dataset_d0ae7d04-556d-48aa-a859-63d0efd9bc1c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/d/2/9/dataset_d293bdbb-5524-4e82-a4a0-d687a407a968.dat:BBa_E0040_GFP.gb,/tmp/tmphxxoceah/files/e/a/5/dataset_ea5e46a6-144f-4c5e-b626-6bca5055f710.dat:BBa_J23119_prom.gb,/tmp/tmphxxoceah/files/b/4/9/dataset_b491036e-78aa-4140-bca6-63462b7dbb5a.dat:BBa_J23119_prom_flawed.gb,/tmp/tmphxxoceah/files/1/c/f/dataset_1cf514a1-2062-47c1-98b3-d86c408d348d.dat:BBa_J61048_term.gb,/tmp/tmphxxoceah/files/d/0/a/dataset_d0ae7d04-556d-48aa-a859-63d0efd9bc1c.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/tmphxxoceah/job_working_directory/000/35/outputs/dataset_4731915b-5562-4afe-b2f2-cf88b2af3eb5.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:57:56.917009", + "create_time": "2025-05-26T09:46:47.832614", "dependencies": [ { "cacheable": false, @@ -1199,41 +1199,41 @@ } ], "exit_code": 0, - "external_id": "80672", + "external_id": "104081", "galaxy_version": "24.2", "handler": null, - "history_id": "48e4779cf88cf124", - "id": "4f510c4214d7d568", + "history_id": "f825d543d1b9cf39", + "id": "4b5a70f26b4819b4", "inputs": { "assembly_csv": { - "id": "017df84d4155fcba", + "id": "6aba8bde83c91d2f", "src": "hda", - "uuid": "fd913c0f-ea98-4b8d-a170-961146c201d5" + "uuid": "2ad0d873-86c6-45d9-b7d2-124dcbc1af89" }, "genbank_files1": { - "id": "1745fab1994e918a", + "id": "1aae5cb645dbaceb", "src": "hda", - "uuid": "38402f39-a1d3-495e-afed-bf8335b4cdb6" + "uuid": "d293bdbb-5524-4e82-a4a0-d687a407a968" }, "genbank_files2": { - "id": "9f4b12edd1240647", + "id": "cc421d01a299ef36", "src": "hda", - "uuid": "9c8ea453-16b9-4b9d-b171-9d5c0322adf9" + "uuid": "ea5e46a6-144f-4c5e-b626-6bca5055f710" }, "genbank_files3": { - "id": "070cf47a9114ebf0", + "id": "1f0503133822f6be", "src": "hda", - "uuid": "31a46fbb-0267-42e3-b9d3-c60804edd30c" + "uuid": "b491036e-78aa-4140-bca6-63462b7dbb5a" }, "genbank_files4": { - "id": "176efb58f023067c", + "id": "f7b46848b0cdcf03", "src": "hda", - "uuid": "e278e6ea-3146-49fa-a4f5-becf766e4f5e" + "uuid": "1cf514a1-2062-47c1-98b3-d86c408d348d" }, "genbank_files5": { - "id": "2c38922866e3bd19", + "id": "c92ddd5b8e0dfe51", "src": "hda", - "uuid": "6a19d37f-54e1-4c94-a2b1-1a7f37820aad" + "uuid": "d0ae7d04-556d-48aa-a859-63d0efd9bc1c" } }, "job_messages": [], @@ -1244,55 +1244,55 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "7ede2556a40dc9ba", + "id": "2bdc7fcb2931f07b", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { - "id": "e9bea5372f4a6a20", + "id": "4e090171f4d7129f", "src": "hda", - "uuid": "80f480c8-264d-428b-8b95-253cd89d7764" + "uuid": "0541aea5-21f7-4b9b-b037-ce0b677829bb" }, "__new_primary_file_construct_gb|C2_gfp_term__": { - "id": "1290d6537f2937e3", + "id": "4a624b810533f2ef", "src": "hda", - "uuid": "7b7b6524-575a-4dfc-800c-dc0d3e8ece79" + "uuid": "381b158b-3536-4150-be35-d3e2b6e5dc19" }, "__new_primary_file_construct_gb|C3_final__": { - "id": "cd293a8cb9d8e7b5", + "id": "99b0b6baf442a2d9", "src": "hda", - "uuid": "7be9e218-0841-46cd-ac62-5686969f6935" + "uuid": "084415f0-529e-443f-bfa9-7ce16f75171f" }, "output_zip": { - "id": "3651b2c7591f0e47", + "id": "a38ed44718641cdb", "src": "hda", - "uuid": "a3f2eab1-bbe1-401e-b436-b7ffc698ee3a" + "uuid": "4731915b-5562-4afe-b2f2-cf88b2af3eb5" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"BioBrickStandardAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "domesticated_input": null, "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", "topology": "\"circular\"" }, "state": "ok", - "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T08:58:09.572798", + "update_time": "2025-05-26T09:47:00.964337", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 4, - "time_seconds": 34.93839716911316, + "time_seconds": 34.59279441833496, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1304,25 +1304,25 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "b1a8f56fe428091e", + "id": "09ac55ab9704eba2", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "76608081d307dc20", + "id": "dc7e3ab6a421767b", "src": "hdca" }, "genbank_files": { - "id": "0551bf01e3dbca02", + "id": "b1d9a1d43e36b679", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/9/7/b/dataset_97b16fa9-53ab-4e65-9de7-e30112bcdd06.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat' --domesticated_seq '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/49/outputs/dataset_2bca238e-5421-456d-bf98-1bd44e65fc76.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/0/d/8/dataset_0d80ec64-7c14-49ec-bf00-8b127413b402.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/b/f/e/dataset_bfe6c5a0-bee9-4fcd-bc48-1030fddae94b.dat,/tmp/tmphxxoceah/files/5/b/1/dataset_5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb.dat,/tmp/tmphxxoceah/files/b/3/e/dataset_b3ecd963-5e7a-4c86-91f3-8d8322471402.dat,/tmp/tmphxxoceah/files/6/f/8/dataset_6f8d0b94-6f0f-470c-b36a-87256aa427c6.dat,/tmp/tmphxxoceah/files/2/f/d/dataset_2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e.dat,/tmp/tmphxxoceah/files/c/5/f/dataset_c5fde1d8-6078-4b1c-946d-fe58c868e1a5.dat,/tmp/tmphxxoceah/files/0/2/0/dataset_0203ce08-8c98-4dcf-a274-ac69f126eb78.dat' --domesticated_seq '/tmp/tmphxxoceah/files/9/0/7/dataset_9073f5ed-6218-436e-9c90-40231a771418.dat,/tmp/tmphxxoceah/files/1/c/2/dataset_1c278033-6add-4e83-92ee-ece6b30d73b2.dat,/tmp/tmphxxoceah/files/6/8/b/dataset_68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6.dat,/tmp/tmphxxoceah/files/e/2/a/dataset_e2abf373-3268-46a0-a6bd-889fe7061984.dat,/tmp/tmphxxoceah/files/d/7/1/dataset_d71d0b7d-fc98-4d97-8a6b-e92bb229582e.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/b/f/e/dataset_bfe6c5a0-bee9-4fcd-bc48-1030fddae94b.dat:part_A.gb,/tmp/tmphxxoceah/files/5/b/1/dataset_5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb.dat:part_B.gb,/tmp/tmphxxoceah/files/b/3/e/dataset_b3ecd963-5e7a-4c86-91f3-8d8322471402.dat:part_C.gb,/tmp/tmphxxoceah/files/6/f/8/dataset_6f8d0b94-6f0f-470c-b36a-87256aa427c6.dat:part_D.gb,/tmp/tmphxxoceah/files/2/f/d/dataset_2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e.dat:part_E.gb,/tmp/tmphxxoceah/files/c/5/f/dataset_c5fde1d8-6078-4b1c-946d-fe58c868e1a5.dat:part_F.gb,/tmp/tmphxxoceah/files/0/2/0/dataset_0203ce08-8c98-4dcf-a274-ac69f126eb78.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmphxxoceah/files/9/0/7/dataset_9073f5ed-6218-436e-9c90-40231a771418.dat:part_H.gb,/tmp/tmphxxoceah/files/1/c/2/dataset_1c278033-6add-4e83-92ee-ece6b30d73b2.dat:part_I.gb,/tmp/tmphxxoceah/files/6/8/b/dataset_68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6.dat:part_J.gb,/tmp/tmphxxoceah/files/e/2/a/dataset_e2abf373-3268-46a0-a6bd-889fe7061984.dat:part_K.gb,/tmp/tmphxxoceah/files/d/7/1/dataset_d71d0b7d-fc98-4d97-8a6b-e92bb229582e.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/tmphxxoceah/job_working_directory/000/49/outputs/dataset_e791efbc-be6b-44c5-a124-a744a812b597.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:58:50.541909", + "create_time": "2025-05-26T09:47:41.246196", "dependencies": [ { "cacheable": false, @@ -1502,76 +1502,76 @@ } ], "exit_code": 0, - "external_id": "81731", + "external_id": "105127", "galaxy_version": "24.2", "handler": null, - "history_id": "2bf3ecab9316a382", - "id": "aa893e5f7beb4eb8", + "history_id": "24f234959abeadac", + "id": "271c0f8150c5b24a", "inputs": { "assembly_csv": { - "id": "b1a8f56fe428091e", + "id": "09ac55ab9704eba2", "src": "hda", - "uuid": "97b16fa9-53ab-4e65-9de7-e30112bcdd06" + "uuid": "0d80ec64-7c14-49ec-bf00-8b127413b402" }, "domesticated_input1": { - "id": "dbc527c8f70438a2", + "id": "f1e670d3230dc49d", "src": "hda", - "uuid": "ef3f0423-f1dd-462b-8d68-e68cd6d59d82" + "uuid": "9073f5ed-6218-436e-9c90-40231a771418" }, "domesticated_input2": { - "id": "a3ea165695c1e088", + "id": "d6d38b30a0e08779", "src": "hda", - "uuid": "ea297609-87c4-4bfc-abfd-084fbcc94d5b" + "uuid": "1c278033-6add-4e83-92ee-ece6b30d73b2" }, "domesticated_input3": { - "id": "d4fcfbec208c480f", + "id": "5df6658d98901785", "src": "hda", - "uuid": "60d919ff-9b54-4856-b3d0-9836114c2575" + "uuid": "68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6" }, "domesticated_input4": { - "id": "b53993d77cff267e", + "id": "179c4c4e78c36c21", "src": "hda", - "uuid": "08efef6d-13c4-4e1b-a155-859e0a0df989" + "uuid": "e2abf373-3268-46a0-a6bd-889fe7061984" }, "domesticated_input5": { - "id": "e1a323c2b9a73ada", + "id": "b1ed244e949762c6", "src": "hda", - "uuid": "e72facc2-0bd8-49e8-94e6-6b255853b030" + "uuid": "d71d0b7d-fc98-4d97-8a6b-e92bb229582e" }, "genbank_files1": { - "id": "03a53f60ebb3b30b", + "id": "faf74795de9215e4", "src": "hda", - "uuid": "823cfc4c-98db-494d-a03b-5181179a3581" + "uuid": "bfe6c5a0-bee9-4fcd-bc48-1030fddae94b" }, "genbank_files2": { - "id": "949b6e5fb08e3b2e", + "id": "982fc2b45c634401", "src": "hda", - "uuid": "60a53b2c-927e-4c33-b6b0-2e927266044e" + "uuid": "5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb" }, "genbank_files3": { - "id": "4b14363353165bd2", + "id": "d49187f9d744460f", "src": "hda", - "uuid": "d357996d-45c3-4715-b8eb-ea6bb836b18e" + "uuid": "b3ecd963-5e7a-4c86-91f3-8d8322471402" }, "genbank_files4": { - "id": "aa893e5f7beb4eb8", + "id": "271c0f8150c5b24a", "src": "hda", - "uuid": "dacfd7e2-f5ff-4821-8d70-f73307f7997e" + "uuid": "6f8d0b94-6f0f-470c-b36a-87256aa427c6" }, "genbank_files5": { - "id": "e33440187009b2c6", + "id": "954a11ecc737c99c", "src": "hda", - "uuid": "9b3f9357-c1cc-43c9-a81c-c100483b3a0d" + "uuid": "2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e" }, "genbank_files6": { - "id": "ef97dc51810891e7", + "id": "c90496f58e5d6dd9", "src": "hda", - "uuid": "5e43150c-3c7c-4072-9720-fdc085cd6d8b" + "uuid": "c5fde1d8-6078-4b1c-946d-fe58c868e1a5" }, "genbank_files7": { - "id": "16b078cfbe5cb4fb", + "id": "9c66fe6132ced54b", "src": "hda", - "uuid": "2de75a41-7673-4cef-aa63-2cf6d9466e8c" + "uuid": "0203ce08-8c98-4dcf-a274-ac69f126eb78" } }, "job_messages": [], @@ -1582,60 +1582,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "0a696a8b22798e06", + "id": "7a37f3397bf88665", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "08065af9f1d51b0a", + "id": "ee6560cff5429b3a", "src": "hda", - "uuid": "4837c85e-ba71-482d-91d1-be3e3179ee5a" + "uuid": "2d9d0878-8a8e-4a76-b4c7-8b2c58007a4c" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "23c03036acf6de8c", + "id": "7faeb5268234c1b7", "src": "hda", - "uuid": "a898af9c-3721-4b84-8ebc-790dc376316c" + "uuid": "d8ead123-b416-446e-bcd7-12d88aa380d8" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "950510fee01c22f4", + "id": "71b5e767ad5c3d19", "src": "hda", - "uuid": "be8dfa79-0421-418a-9822-af3e69e3bd0a" + "uuid": "d3370005-e04e-41fe-91ca-5ae418062a9f" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "abd47de82fbecc4e", + "id": "07cc2539cb83a207", "src": "hda", - "uuid": "1455799d-9a0a-46e7-8ddb-df60f983fb53" + "uuid": "0a5f7883-f82b-4122-a882-76fadc52a358" }, "output_zip": { - "id": "b52f373b44c22024", + "id": "49de8d939dbbcfba", "src": "hda", - "uuid": "2bca238e-5421-456d-bf98-1bd44e65fc76" + "uuid": "e791efbc-be6b-44c5-a124-a744a812b597" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/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, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", + "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/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, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", + "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/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": "2025-05-26T08:59:03.629936", + "update_time": "2025-05-26T09:47:53.960080", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 5, - "time_seconds": 53.84836268424988, + "time_seconds": 52.97593927383423, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, @@ -1647,21 +1647,21 @@ "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { - "id": "4b6130eb686f10a7", + "id": "e8ab24d23dab7d7f", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { - "id": "2ff5b0f6b4cfbb73", + "id": "dfd75d2f0da631b2", "src": "hdca" }, "topology": "circular" }, "job": { - "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/0/4/dataset_5042213c-8bb6-48e0-9501-070e55a9a8c0.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp_ibkdcj0/job_working_directory/000/63/outputs/dataset_4e39f3b7-2899-410e-a32f-47270970ae14.dat'", + "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/0/1/7/dataset_017ccfd4-4d46-44c1-99ad-af18724cfa9c.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/c/2/6/dataset_c26ad39f-1237-4c04-8f7f-73d2c5d9ad58.dat,/tmp/tmphxxoceah/files/c/6/8/dataset_c68beeb3-949a-4a3e-ab43-987831504001.dat,/tmp/tmphxxoceah/files/8/f/6/dataset_8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72.dat,/tmp/tmphxxoceah/files/1/0/6/dataset_1069bd61-49fb-492a-8eaf-d98e496576a8.dat,/tmp/tmphxxoceah/files/3/1/1/dataset_311db06e-881c-4a38-9fe9-a13712004ece.dat,/tmp/tmphxxoceah/files/7/8/1/dataset_781cdd92-6baf-451e-8e72-f05961154dae.dat,/tmp/tmphxxoceah/files/7/1/7/dataset_717f7fe8-1fbf-4394-aeff-14d7aa430193.dat,/tmp/tmphxxoceah/files/3/a/8/dataset_3a883d96-6381-4569-a872-6490a47980b2.dat,/tmp/tmphxxoceah/files/c/1/d/dataset_c1d48747-8d18-4249-8b11-60a73ad7446f.dat,/tmp/tmphxxoceah/files/0/e/4/dataset_0e4a4a05-7265-4844-9d70-1ad96facfdf9.dat,/tmp/tmphxxoceah/files/9/f/7/dataset_9f72d140-3946-4567-8ecb-056458d7bb70.dat,/tmp/tmphxxoceah/files/b/6/a/dataset_b6a06ac7-2240-4f68-9e75-63de3f5d10f2.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/c/2/6/dataset_c26ad39f-1237-4c04-8f7f-73d2c5d9ad58.dat:part_A.gb,/tmp/tmphxxoceah/files/c/6/8/dataset_c68beeb3-949a-4a3e-ab43-987831504001.dat:part_B.gb,/tmp/tmphxxoceah/files/8/f/6/dataset_8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72.dat:part_C.gb,/tmp/tmphxxoceah/files/1/0/6/dataset_1069bd61-49fb-492a-8eaf-d98e496576a8.dat:part_D.gb,/tmp/tmphxxoceah/files/3/1/1/dataset_311db06e-881c-4a38-9fe9-a13712004ece.dat:part_E.gb,/tmp/tmphxxoceah/files/7/8/1/dataset_781cdd92-6baf-451e-8e72-f05961154dae.dat:part_F.gb,/tmp/tmphxxoceah/files/7/1/7/dataset_717f7fe8-1fbf-4394-aeff-14d7aa430193.dat:part_G.gb,/tmp/tmphxxoceah/files/3/a/8/dataset_3a883d96-6381-4569-a872-6490a47980b2.dat:part_H.gb,/tmp/tmphxxoceah/files/c/1/d/dataset_c1d48747-8d18-4249-8b11-60a73ad7446f.dat:part_I.gb,/tmp/tmphxxoceah/files/0/e/4/dataset_0e4a4a05-7265-4844-9d70-1ad96facfdf9.dat:part_J.gb,/tmp/tmphxxoceah/files/9/f/7/dataset_9f72d140-3946-4567-8ecb-056458d7bb70.dat:part_K.gb,/tmp/tmphxxoceah/files/b/6/a/dataset_b6a06ac7-2240-4f68-9e75-63de3f5d10f2.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/tmphxxoceah/job_working_directory/000/63/outputs/dataset_9593abfa-a9bc-4a45-8334-5203050a6ca5.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-05-26T08:59:44.629082", + "create_time": "2025-05-26T09:48:34.329479", "dependencies": [ { "cacheable": false, @@ -1841,76 +1841,76 @@ } ], "exit_code": 0, - "external_id": "82808", + "external_id": "106213", "galaxy_version": "24.2", "handler": null, - "history_id": "d51bf47fbc922335", - "id": "abd47de82fbecc4e", + "history_id": "67e443cb5516c0e0", + "id": "07cc2539cb83a207", "inputs": { "assembly_csv": { - "id": "4b6130eb686f10a7", + "id": "e8ab24d23dab7d7f", "src": "hda", - "uuid": "5042213c-8bb6-48e0-9501-070e55a9a8c0" + "uuid": "017ccfd4-4d46-44c1-99ad-af18724cfa9c" }, "domesticated_input1": { - "id": "7c76f7472621b5d0", + "id": "548eebef94e3a53d", "src": "hda", - "uuid": "dd8d9744-d7f0-46ae-b26f-de961e3f5033" + "uuid": "c26ad39f-1237-4c04-8f7f-73d2c5d9ad58" }, "domesticated_input10": { - "id": "9bd6c123148263b6", + "id": "9e9d5c19538ef8ad", "src": "hda", - "uuid": "d2492f3b-8ea9-40e7-8bda-a15b506a22ac" + "uuid": "0e4a4a05-7265-4844-9d70-1ad96facfdf9" }, "domesticated_input11": { - "id": "5d3d21e362e05995", + "id": "8c0e43d479b6b17a", "src": "hda", - "uuid": "3a857675-027c-4b28-bf69-7591db569213" + "uuid": "9f72d140-3946-4567-8ecb-056458d7bb70" }, "domesticated_input12": { - "id": "043b0e9e9cf8c91c", + "id": "b75b41451f2f7195", "src": "hda", - "uuid": "26df2c50-4cbe-45f5-ba07-be8fb89cfb7c" + "uuid": "b6a06ac7-2240-4f68-9e75-63de3f5d10f2" }, "domesticated_input2": { - "id": "11e2d0eceb639139", + "id": "f1612d32ca625e37", "src": "hda", - "uuid": "aa64d9f2-f351-4776-aab6-648a5fa5f6da" + "uuid": "c68beeb3-949a-4a3e-ab43-987831504001" }, "domesticated_input3": { - "id": "991f793af87d39c4", + "id": "bf5687b995aa6663", "src": "hda", - "uuid": "1dbca58c-bd12-48c7-bbfe-49ef8801f8c3" + "uuid": "8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72" }, "domesticated_input4": { - "id": "3429ba0772b9ca69", + "id": "13ae5fed3f9ef282", "src": "hda", - "uuid": "d396d7df-8e9d-441b-b04e-abaaa0c90a7f" + "uuid": "1069bd61-49fb-492a-8eaf-d98e496576a8" }, "domesticated_input5": { - "id": "c04c164ed0056d43", + "id": "58d09772df305f7c", "src": "hda", - "uuid": "4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a" + "uuid": "311db06e-881c-4a38-9fe9-a13712004ece" }, "domesticated_input6": { - "id": "b3ed12fa60bc840b", + "id": "940c0a8788b53ef0", "src": "hda", - "uuid": "2e907739-181d-44bc-8bc4-35d252e00535" + "uuid": "781cdd92-6baf-451e-8e72-f05961154dae" }, "domesticated_input7": { - "id": "5406c597edc1a692", + "id": "5d12b487c622fea5", "src": "hda", - "uuid": "9d3053e2-630d-4fba-9b08-09f59013ab96" + "uuid": "717f7fe8-1fbf-4394-aeff-14d7aa430193" }, "domesticated_input8": { - "id": "780d322efdca3fcd", + "id": "7f6a5e9bab73b744", "src": "hda", - "uuid": "26364877-f482-4b4d-8346-61a2f50f1ccf" + "uuid": "3a883d96-6381-4569-a872-6490a47980b2" }, "domesticated_input9": { - "id": "951610fc65ac475f", + "id": "917d245d020dcffb", "src": "hda", - "uuid": "6f64f828-be8e-4e72-a940-87396256fe3f" + "uuid": "c1d48747-8d18-4249-8b11-60a73ad7446f" } }, "job_messages": [], @@ -1921,60 +1921,60 @@ "model_class": "Job", "output_collections": { "construct_gb": { - "id": "be5466d8eb2c2229", + "id": "cecf675ce2a554e8", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { - "id": "6d4b50576bf02b31", + "id": "6ed4cf4ef5da4ab6", "src": "hda", - "uuid": "d4f04f5f-16a6-4675-a892-fa6d05156592" + "uuid": "77c80040-9366-4df3-8ee7-b8f5c6148b73" }, "__new_primary_file_construct_gb|construct_2__": { - "id": "550e95bf5471ae1d", + "id": "f0c0b63c8f5e218a", "src": "hda", - "uuid": "845f0e19-1541-481b-a386-47135e8ebdf1" + "uuid": "8a7bd174-630d-439e-a111-682129e2dbc6" }, "__new_primary_file_construct_gb|construct_3__": { - "id": "359048b3278e74c9", + "id": "89c8871118f8304b", "src": "hda", - "uuid": "420b6912-da3c-4b75-ae88-b73f0c005864" + "uuid": "5ee7450c-795c-4a27-8354-25ac7ab1d71f" }, "__new_primary_file_construct_gb|construct_4__": { - "id": "7a3e4925ca1f5f1d", + "id": "57b71ad05e041af6", "src": "hda", - "uuid": "5b639734-e44b-415c-b347-5a702df97945" + "uuid": "b3b86695-7ea9-43e6-bfbb-6a20972dec20" }, "output_zip": { - "id": "40a6167ab839cf08", + "id": "2ec06dcf804a9f1d", "src": "hda", - "uuid": "4e39f3b7-2899-410e-a32f-47270970ae14" + "uuid": "9593abfa-a9bc-4a45-8334-5203050a6ca5" } }, "params": { "__input_ext": "\"input\"", "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmphxxoceah/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, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", + "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, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", "tool_id": "cloning_simulation", - "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/s, now=None]\r \r", + "tool_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, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", - "update_time": "2025-05-26T08:59:57.832603", + "update_time": "2025-05-26T09:48:47.319875", "user_email": "planemo@galaxyproject.org", - "user_id": "cb6d3fbb91be6861" + "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 6, - "time_seconds": 53.99832892417908, + "time_seconds": 53.241769552230835, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" },