Mercurial > repos > tduigou > cloning_simulation
view output.json @ 14:16ccb36aa8e3 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 11:29:13 +0000 |
| parents | 7d1778f5e164 |
| children | 074a76e84b80 |
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{ "summary": { "num_errors": 0, "num_failures": 0, "num_skips": 0, "num_tests": 7 }, "tests": [ { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "c173cff58a987f8f", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "fcc5b7d13a1328f6", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:24:01.275241", "dependencies": [], "exit_code": 0, "external_id": "151844", "galaxy_version": "24.2", "handler": null, "history_id": "fcc5b7d13a1328f6", "id": "c9445e550eef23d0", "inputs": { "assembly_csv": { "id": "c173cff58a987f8f", "src": "hda", "uuid": "2bdf436f-52cc-4c6e-afdb-3f051629900f" }, "genbank_files1": { "id": "fcc5b7d13a1328f6", "src": "hda", "uuid": "465a53ab-8770-4514-a9b3-227f79646eb7" }, "genbank_files10": { "id": "cf75f655bb15877b", "src": "hda", "uuid": "95699db9-77cf-4ae1-8454-4f255f3cb62a" }, "genbank_files11": { "id": "744832bdd7ccd728", "src": "hda", "uuid": "11979c28-82ee-43c4-9e43-f34cb541f96b" }, "genbank_files12": { "id": "855b83dd0dec8eab", "src": "hda", "uuid": "3f53cb86-2d2b-429a-bf51-e276bbe393fa" }, "genbank_files2": { "id": "df00a2d9def0cc87", "src": "hda", "uuid": "ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa" }, "genbank_files3": { "id": "d9e72a80becfe6e7", "src": "hda", "uuid": "e64057b1-43b3-4788-8891-77bcd297223c" }, "genbank_files4": { "id": "038c626e299361e9", "src": "hda", "uuid": "1d1f9832-b58e-48c2-b1b3-6c3fb18e9890" }, "genbank_files5": { "id": "c7c3cd49f3337c1a", "src": "hda", "uuid": "6732fc79-081e-4edf-bccc-a0087520172a" }, "genbank_files6": { "id": "51c35891e43131e2", "src": "hda", "uuid": "b17c7a49-3121-4292-95ff-51891aa066d1" }, "genbank_files7": { "id": "84db48b219855f4d", "src": "hda", "uuid": "2811f816-8532-4ddd-8e29-9a6ed7dad54e" }, "genbank_files8": { "id": "cf00b67a5455eb5a", "src": "hda", "uuid": "e74d0182-807e-40a8-b67a-ac088fc2e02c" }, "genbank_files9": { "id": "a3780ecc1a00a0d8", "src": "hda", "uuid": "9dc55c98-4ab9-4272-a680-9b3129954367" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "df00a2d9def0cc87", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "fedb85639c7c80b9", "src": "hda", "uuid": "4bf90377-e4de-4d13-8ebc-39a53494ea2a" }, "__new_primary_file_construct_gb|construct_2__": { "id": "bd75ec7b3d9705ea", "src": "hda", "uuid": "ac9bac0c-348b-46b7-a882-60f56867cc30" }, "__new_primary_file_construct_gb|construct_3__": { "id": "7eb30039064fccdd", "src": "hda", "uuid": "48e39545-a44e-410b-859b-01fcf6189002" }, "__new_primary_file_construct_gb|construct_4__": { "id": "61cc0a7b70456dfd", "src": "hda", "uuid": "df8aca7f-8413-430f-b35f-7dac694ee0b6" }, "output_zip": { "id": "c9445e550eef23d0", "src": "hda", "uuid": "ac2d98e7-ff55-4a94-9e79-861b07d63528" } }, "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\"", "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", "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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 0, "time_seconds": 53.70547914505005, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-0" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "3af58a5242e85ea6", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "d9e72a80becfe6e7", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:24:25.394299", "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": "152204", "galaxy_version": "24.2", "handler": null, "history_id": "df00a2d9def0cc87", "id": "7eb30039064fccdd", "inputs": { "assembly_csv": { "id": "3af58a5242e85ea6", "src": "hda", "uuid": "1d624c24-e864-463a-9fd3-0c63fd46cbd2" }, "genbank_files1": { "id": "3b85967b9c87a1cc", "src": "hda", "uuid": "505aafa2-5e9c-44bb-9d26-3f3e6248fc9b" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "038c626e299361e9", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "9773f41fb184880d", "src": "hda", "uuid": "0d66c887-a6a3-4fd6-978a-9c0e2ce4b317" }, "__new_primary_file_construct_gb|construct_2__": { "id": "41b44b0c750630a6", "src": "hda", "uuid": "be7e7183-3b0d-40dd-9908-3e8dcd7f80bf" }, "__new_primary_file_construct_gb|construct_3__": { "id": "bfc60c3d9bac68ee", "src": "hda", "uuid": "2c7f645c-33d1-4a91-9608-221494b22be4" }, "output_zip": { "id": "5c8c8c874b5b07c6", "src": "hda", "uuid": "0f617192-e625-4d9e-8358-0b9b1b0aa024" } }, "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\"", "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", "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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 1, "time_seconds": 22.626197814941406, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-1" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "48d1542b43af9171", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "c7c3cd49f3337c1a", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:24:49.729783", "dependencies": [], "exit_code": 0, "external_id": "152654", "galaxy_version": "24.2", "handler": null, "history_id": "d9e72a80becfe6e7", "id": "5c8c8c874b5b07c6", "inputs": { "assembly_csv": { "id": "48d1542b43af9171", "src": "hda", "uuid": "a1f989b9-e79f-4bd7-9cf3-66675c1d1e94" }, "genbank_files1": { "id": "b8df5ed9fe071f18", "src": "hda", "uuid": "a617ae1f-70e3-4873-bdcc-f2268ffeaad4" }, "genbank_files2": { "id": "6de9142d4b5ca725", "src": "hda", "uuid": "941b4e95-600a-485c-a3fa-1dcf0defdd76" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "51c35891e43131e2", "src": "hdca" } }, "outputs": { "output_zip": { "id": "56521fbfdcb4ef20", "src": "hda", "uuid": "827e64a1-7f84-4f9e-8468-eabb3684efa3" } }, "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\"", "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", "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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 2, "time_seconds": 24.395533084869385, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-2" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "2b17a3fa18c23b8a", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "84db48b219855f4d", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:25:23.055332", "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": "153248", "galaxy_version": "24.2", "handler": null, "history_id": "038c626e299361e9", "id": "56521fbfdcb4ef20", "inputs": { "assembly_csv": { "id": "2b17a3fa18c23b8a", "src": "hda", "uuid": "6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc" }, "genbank_files1": { "id": "aed8b1a22d89d8c9", "src": "hda", "uuid": "cba9b297-4dfe-4063-8510-6c48a1b6b7a1" }, "genbank_files2": { "id": "eba7a310b55aafdd", "src": "hda", "uuid": "3e8dfce1-7a05-4665-9277-388e3aa42581" }, "genbank_files3": { "id": "eca1089322e0a5fc", "src": "hda", "uuid": "a5d093c2-0087-453e-b7d1-d94a7cb664e0" }, "genbank_files4": { "id": "0b586e83183b9891", "src": "hda", "uuid": "0ec72cc0-2a95-474b-aa77-7a436dad6a9b" }, "genbank_files5": { "id": "18d15f79e0c5cee5", "src": "hda", "uuid": "d272199f-2e1b-49e1-a597-5ffa11507e83" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "cf00b67a5455eb5a", "src": "hdca" } }, "outputs": { "output_zip": { "id": "684e8d7e5eb8731e", "src": "hda", "uuid": "7435335e-896e-47f4-89c7-3a6c2c25f247" } }, "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\"", "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", "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_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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 3, "time_seconds": 30.88078260421753, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-3" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "8484dc7b019fd65a", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "a3780ecc1a00a0d8", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:25:53.885012", "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": "153816", "galaxy_version": "24.2", "handler": null, "history_id": "c7c3cd49f3337c1a", "id": "684e8d7e5eb8731e", "inputs": { "assembly_csv": { "id": "8484dc7b019fd65a", "src": "hda", "uuid": "8e2dcaab-3dd7-48c4-920e-bdffaad39793" }, "genbank_files1": { "id": "f007b0e97c7852a9", "src": "hda", "uuid": "d4271a43-8722-4344-9562-00e9a36d07e5" }, "genbank_files2": { "id": "0776247cf19fcdeb", "src": "hda", "uuid": "2484bbfb-d4b0-4c8b-a57f-675625f98753" }, "genbank_files3": { "id": "428c69cf899eb78e", "src": "hda", "uuid": "83f035f7-25fc-4a59-83b2-d377e3cd59ad" }, "genbank_files4": { "id": "6576e427b69a444e", "src": "hda", "uuid": "5aa7b19e-0ad1-43b1-9083-954067ff2010" }, "genbank_files5": { "id": "bd5ff021b11f5160", "src": "hda", "uuid": "d646b71c-5393-4291-bcc5-7d6cbe22f055" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "cf75f655bb15877b", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "db302e29238adc09", "src": "hda", "uuid": "d9b71247-a39f-49ea-b279-18a95173730d" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "a0c89ee18eccf84a", "src": "hda", "uuid": "cf4710c7-cf67-4f0e-a486-606e525f5689" }, "__new_primary_file_construct_gb|C3_final__": { "id": "b326684e3f9ff9a4", "src": "hda", "uuid": "a4ed1a6f-9385-45da-9eda-3fae86d46b5b" }, "output_zip": { "id": "e3a5c74dec901fc5", "src": "hda", "uuid": "8086c8c0-24b8-4a51-84db-6b4c9b0e76d0" } }, "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\"", "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", "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_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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 4, "time_seconds": 33.60218787193298, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-4" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "ffdd8176dffd877d", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "744832bdd7ccd728", "src": "hdca" }, "genbank_files": { "id": "855b83dd0dec8eab", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:26:47.030790", "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": "154908", "galaxy_version": "24.2", "handler": null, "history_id": "51c35891e43131e2", "id": "0b19a103e85bbfbf", "inputs": { "assembly_csv": { "id": "ffdd8176dffd877d", "src": "hda", "uuid": "98e1b862-2d3e-4164-aecf-56bd464d0f11" }, "domesticated_input1": { "id": "96e47893a0f61173", "src": "hda", "uuid": "6877c227-2c70-4080-962e-ee1855dd797f" }, "domesticated_input2": { "id": "07b1a06cea2f6611", "src": "hda", "uuid": "e212262c-a336-4263-a076-2cd300590ba4" }, "domesticated_input3": { "id": "7c42ebb9622f8a60", "src": "hda", "uuid": "4112d545-7e37-4a6e-8ca8-7c1b8f90a71e" }, "domesticated_input4": { "id": "33456f383510d381", "src": "hda", "uuid": "b31955ce-ea44-4e3a-86a1-6aebc47be841" }, "domesticated_input5": { "id": "3c2a17e7ec6c065d", "src": "hda", "uuid": "d4d14388-55d3-4aec-810d-aa902028f29f" }, "genbank_files1": { "id": "c2ddc784389f17d2", "src": "hda", "uuid": "b66afa5b-682d-49f8-9753-c78c356ff228" }, "genbank_files2": { "id": "79b5ff6df7bc6716", "src": "hda", "uuid": "46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c" }, "genbank_files3": { "id": "6f172ec7c3220722", "src": "hda", "uuid": "8358e657-0e61-486b-adb4-e886f0f354ba" }, "genbank_files4": { "id": "0b19a103e85bbfbf", "src": "hda", "uuid": "4cfbb2dd-c5a5-42fe-889b-da6510422b72" }, "genbank_files5": { "id": "00fa99289b8a441d", "src": "hda", "uuid": "28c96444-abfb-4173-970e-e895146aef97" }, "genbank_files6": { "id": "95a08e54dcf8e4b4", "src": "hda", "uuid": "f54c7a16-ac6f-42c2-9b6c-345af3050d83" }, "genbank_files7": { "id": "46fceb9ab6cb9139", "src": "hda", "uuid": "2a330eb7-d033-4e75-be7a-4473748a6f2d" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "c173cff58a987f8f", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "887639ccacb877d4", "src": "hda", "uuid": "ac0f5082-55fc-4fb6-b3ef-f2587cdd2662" }, "__new_primary_file_construct_gb|construct_2__": { "id": "97c509c62c06ea77", "src": "hda", "uuid": "9e439105-9563-450d-96a3-bec58242389e" }, "__new_primary_file_construct_gb|construct_3__": { "id": "05372c5ab71bbd4d", "src": "hda", "uuid": "13079e9f-8185-4b43-898a-83348a3fe55b" }, "__new_primary_file_construct_gb|construct_4__": { "id": "14e667eccbf3c9ac", "src": "hda", "uuid": "4aec2395-19a8-49b5-a927-39b5b06dabe7" }, "output_zip": { "id": "edb47c5501e52d48", "src": "hda", "uuid": "77f39d12-532c-468b-bcf7-fcc1fdedd34c" } }, "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\"", "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", "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_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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 5, "time_seconds": 53.75153422355652, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-5" }, { "data": { "inputs": { "adv|use_file_names_as_ids": true, "assembly_csv": { "id": "59a0a00f5fa501d5", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "c9445e550eef23d0", "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_version": "", "copied_from_job_id": null, "create_time": "2025-05-26T11:27:41.184534", "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": "155964", "galaxy_version": "24.2", "handler": null, "history_id": "84db48b219855f4d", "id": "14e667eccbf3c9ac", "inputs": { "assembly_csv": { "id": "59a0a00f5fa501d5", "src": "hda", "uuid": "9504897d-0d99-44a4-9033-7d14e3943ec9" }, "domesticated_input1": { "id": "2252f6534dc04be9", "src": "hda", "uuid": "acd9e546-bb31-4391-b867-1d81cab10920" }, "domesticated_input10": { "id": "b26f1eae65161bae", "src": "hda", "uuid": "1b480e84-03cf-4483-9e9e-ccf79bf654a1" }, "domesticated_input11": { "id": "748ef145f2d110fe", "src": "hda", "uuid": "be83b8f4-73de-4775-abb8-75483d4e8ab2" }, "domesticated_input12": { "id": "37a05bd56b325e88", "src": "hda", "uuid": "5ddde548-4828-4067-93b7-1377a71221d7" }, "domesticated_input2": { "id": "2441550d408330ea", "src": "hda", "uuid": "cfe852f6-5b32-46fd-a9d8-2b777016d403" }, "domesticated_input3": { "id": "7982f5ab86225272", "src": "hda", "uuid": "25be2770-f768-4b0e-be96-459e47e6ae8d" }, "domesticated_input4": { "id": "1d0be35bf9fc6600", "src": "hda", "uuid": "e580f806-e8ba-4dac-b8d5-6b76b4a7421b" }, "domesticated_input5": { "id": "40fe86a604adcf6d", "src": "hda", "uuid": "0d6de31a-aab1-427f-a2a1-7c8bc988208e" }, "domesticated_input6": { "id": "7355915c318fd136", "src": "hda", "uuid": "1272b23f-7cef-4deb-bf92-fbad973bf2c6" }, "domesticated_input7": { "id": "bacbde4487432826", "src": "hda", "uuid": "7476b10d-c143-4be7-adb5-118dcf372287" }, "domesticated_input8": { "id": "3b9b440d32d1c6f3", "src": "hda", "uuid": "e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a" }, "domesticated_input9": { "id": "a19ae27f3bb8e8c1", "src": "hda", "uuid": "ca18b50c-3b4c-4201-88b0-dffd049718f8" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "fedb85639c7c80b9", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "94b6b8378debd859", "src": "hda", "uuid": "5145585f-443e-4934-af0b-60e1552a08a9" }, "__new_primary_file_construct_gb|construct_2__": { "id": "dfa4bbdeadf76cd3", "src": "hda", "uuid": "6f0dcaec-2131-4c0c-820b-bb5c895103e2" }, "__new_primary_file_construct_gb|construct_3__": { "id": "e48032fd92b02fbb", "src": "hda", "uuid": "8c4da7fd-9c6b-4430-9444-c6e89b41c5df" }, "__new_primary_file_construct_gb|construct_4__": { "id": "68bf450f38f03a28", "src": "hda", "uuid": "a878e0a8-6f34-4cdf-8990-e178d0f15d52" }, "output_zip": { "id": "1062de4bcda0d565", "src": "hda", "uuid": "e10784a6-3050-4131-a684-3847397c4c4d" } }, "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\"", "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", "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_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", "user_email": "planemo@galaxyproject.org", "user_id": "fcc5b7d13a1328f6" }, "status": "success", "test_index": 6, "time_seconds": 53.42731332778931, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-6" } ], "version": "0.1" }