Mercurial > repos > tduigou > cloning_simulation
view output.json @ 11:be6889ab2df8 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 26 May 2025 09:54:05 +0000 |
| parents | 0be569bd5443 |
| children | 7d1778f5e164 |
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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": "7a37f3397bf88665", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "genbank_files": { "id": "b5f519d254c4f536", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:44:56.264493", "dependencies": [], "exit_code": 0, "external_id": "102136", "galaxy_version": "24.2", "handler": null, "history_id": "b5f519d254c4f536", "id": "dfd75d2f0da631b2", "inputs": { "assembly_csv": { "id": "7a37f3397bf88665", "src": "hda", "uuid": "61aa4b8a-d71a-4e9d-a878-5f0d1494b36d" }, "genbank_files1": { "id": "b5f519d254c4f536", "src": "hda", "uuid": "fce5b5a1-92e2-4c39-90d5-0eddf56635f0" }, "genbank_files10": { "id": "2bdc7fcb2931f07b", "src": "hda", "uuid": "387ad7a6-1931-4a46-99d5-4513ba93a999" }, "genbank_files11": { "id": "dc7e3ab6a421767b", "src": "hda", "uuid": "6829a587-673a-44a6-8bcf-ec6334a9184f" }, "genbank_files12": { "id": "b1d9a1d43e36b679", "src": "hda", "uuid": "40405cee-d70a-45d6-ac91-05616fe798b9" }, "genbank_files2": { "id": "c5accd210dc5c9dd", "src": "hda", "uuid": "a6400a83-e4fd-488b-94e8-5ec1f44db9ca" }, "genbank_files3": { "id": "10fbf206fb2087c4", "src": "hda", "uuid": "a66c7ac9-f828-405d-9a49-842e978b00af" }, "genbank_files4": { "id": "27fa0815bff520f2", "src": "hda", "uuid": "54b878ab-05e6-4212-b399-ab1f62c59e16" }, "genbank_files5": { "id": "f825d543d1b9cf39", "src": "hda", "uuid": "39021efe-6a4f-4b7f-ba0d-f87c2b436a0f" }, "genbank_files6": { "id": "24f234959abeadac", "src": "hda", "uuid": "be26c9ab-28e8-449a-bd01-2047af0dfa5d" }, "genbank_files7": { "id": "67e443cb5516c0e0", "src": "hda", "uuid": "f7fd1975-81bc-4a4f-89c6-d946d59782ee" }, "genbank_files8": { "id": "5180b1a726879d60", "src": "hda", "uuid": "fb1f0888-2487-4f14-bcdd-fa06923d4cd9" }, "genbank_files9": { "id": "c3b441e1ed1e9870", "src": "hda", "uuid": "250500a7-25ca-4cba-8d71-7d16053afcaa" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "c5accd210dc5c9dd", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "cecf675ce2a554e8", "src": "hda", "uuid": "3f70ca65-7fb8-4f83-b6e7-3f9893b1db5e" }, "__new_primary_file_construct_gb|construct_2__": { "id": "9cc1fc667f1eccc7", "src": "hda", "uuid": "723df0ab-a674-4b94-b805-15e38f56cbd5" }, "__new_primary_file_construct_gb|construct_3__": { "id": "0b28ef6dfa05b9a4", "src": "hda", "uuid": "0225d884-89af-4b29-bf0c-d27e776614a3" }, "__new_primary_file_construct_gb|construct_4__": { "id": "dd0a4ddfadd2b33c", "src": "hda", "uuid": "2495d80c-1c1d-4aa7-af8c-eac0dd199af2" }, "output_zip": { "id": "dfd75d2f0da631b2", "src": "hda", "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/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, 2.42it/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, 2.42it/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": "2025-05-26T09:45:09.253153", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 0, "time_seconds": 53.940672636032104, "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": "191f29e52861c771", "src": "hda" }, "assembly_plan_name": "GibsonAssembly", "genbank_files": { "id": "10fbf206fb2087c4", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:45:19.833949", "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": "102481", "galaxy_version": "24.2", "handler": null, "history_id": "c5accd210dc5c9dd", "id": "0b28ef6dfa05b9a4", "inputs": { "assembly_csv": { "id": "191f29e52861c771", "src": "hda", "uuid": "ae19b93d-96dc-4575-922e-1c1b13cdda00" }, "genbank_files1": { "id": "1bd551c439d3389f", "src": "hda", "uuid": "66becc5b-d90e-4bca-8456-82d9f7c209ea" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "27fa0815bff520f2", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "a74d82facdf691d6", "src": "hda", "uuid": "d06a3b4e-424a-4af4-b067-8426c2170c90" }, "__new_primary_file_construct_gb|construct_2__": { "id": "7d2e9c5805bbd6ea", "src": "hda", "uuid": "1f95f8b0-5fc6-4b06-9550-06dd8233e6bd" }, "__new_primary_file_construct_gb|construct_3__": { "id": "6c4aee794b3972b4", "src": "hda", "uuid": "cfd50000-e85e-4b17-985e-f137dc59b08b" }, "output_zip": { "id": "e670fc59d69da207", "src": "hda", "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/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, 4.35it/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, 4.35it/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": "2025-05-26T09:45:31.869394", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 1, "time_seconds": 22.247495412826538, "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": "83c94260ae237f16", "src": "hda" }, "assembly_plan_name": "LigaseCyclingReactionAssembly", "genbank_files": { "id": "f825d543d1b9cf39", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:45:42.951843", "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": "102861", "galaxy_version": "24.2", "handler": null, "history_id": "10fbf206fb2087c4", "id": "e670fc59d69da207", "inputs": { "assembly_csv": { "id": "83c94260ae237f16", "src": "hda", "uuid": "82c2d90b-0ca3-4633-915b-eaa0ab81b80f" }, "genbank_files1": { "id": "57b57ab024b6e67d", "src": "hda", "uuid": "cbf24487-bf9d-469a-99cd-bccebb2bc139" }, "genbank_files2": { "id": "71d78516c0fe784e", "src": "hda", "uuid": "d3d42e4b-1982-4660-8ad4-f12c8a0599cb" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "24f234959abeadac", "src": "hdca" } }, "outputs": { "output_zip": { "id": "1211f83788e0a9a2", "src": "hda", "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/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, 2.38it/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, 2.38it/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": "2025-05-26T09:45:54.473182", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 2, "time_seconds": 22.476279258728027, "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": "2aab5679a1ae5c57", "src": "hda" }, "assembly_plan_name": "BASICAssembly", "genbank_files": { "id": "67e443cb5516c0e0", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:46:15.589461", "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": "103494", "galaxy_version": "24.2", "handler": null, "history_id": "27fa0815bff520f2", "id": "1211f83788e0a9a2", "inputs": { "assembly_csv": { "id": "2aab5679a1ae5c57", "src": "hda", "uuid": "2c3186df-93d9-4d24-8956-c6a17e7d822a" }, "genbank_files1": { "id": "0164abbd74b9b05d", "src": "hda", "uuid": "1d824d9e-0b4f-4a81-af49-1acb506e8f4b" }, "genbank_files2": { "id": "f5f5feeed891820d", "src": "hda", "uuid": "57d780ae-3783-4cdf-a295-642ebc88a60e" }, "genbank_files3": { "id": "b3161e3b65353042", "src": "hda", "uuid": "b89b536e-e310-470d-bddc-cd2847c2cfff" }, "genbank_files4": { "id": "292aa45e4e016cce", "src": "hda", "uuid": "bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8" }, "genbank_files5": { "id": "9318ef3621fbfa11", "src": "hda", "uuid": "06587a95-951c-4c6f-bded-3df9fd38a5d1" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "5180b1a726879d60", "src": "hdca" } }, "outputs": { "output_zip": { "id": "4b5a70f26b4819b4", "src": "hda", "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/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, 49.32it/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, 49.32it/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": "2025-05-26T09:46:26.255886", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 3, "time_seconds": 31.84161639213562, "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": "6aba8bde83c91d2f", "src": "hda" }, "assembly_plan_name": "BioBrickStandardAssembly", "genbank_files": { "id": "c3b441e1ed1e9870", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:46:47.832614", "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": "104081", "galaxy_version": "24.2", "handler": null, "history_id": "f825d543d1b9cf39", "id": "4b5a70f26b4819b4", "inputs": { "assembly_csv": { "id": "6aba8bde83c91d2f", "src": "hda", "uuid": "2ad0d873-86c6-45d9-b7d2-124dcbc1af89" }, "genbank_files1": { "id": "1aae5cb645dbaceb", "src": "hda", "uuid": "d293bdbb-5524-4e82-a4a0-d687a407a968" }, "genbank_files2": { "id": "cc421d01a299ef36", "src": "hda", "uuid": "ea5e46a6-144f-4c5e-b626-6bca5055f710" }, "genbank_files3": { "id": "1f0503133822f6be", "src": "hda", "uuid": "b491036e-78aa-4140-bca6-63462b7dbb5a" }, "genbank_files4": { "id": "f7b46848b0cdcf03", "src": "hda", "uuid": "1cf514a1-2062-47c1-98b3-d86c408d348d" }, "genbank_files5": { "id": "c92ddd5b8e0dfe51", "src": "hda", "uuid": "d0ae7d04-556d-48aa-a859-63d0efd9bc1c" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "2bdc7fcb2931f07b", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|C1_prom_barcode__": { "id": "4e090171f4d7129f", "src": "hda", "uuid": "0541aea5-21f7-4b9b-b037-ce0b677829bb" }, "__new_primary_file_construct_gb|C2_gfp_term__": { "id": "4a624b810533f2ef", "src": "hda", "uuid": "381b158b-3536-4150-be35-d3e2b6e5dc19" }, "__new_primary_file_construct_gb|C3_final__": { "id": "99b0b6baf442a2d9", "src": "hda", "uuid": "084415f0-529e-443f-bfa9-7ce16f75171f" }, "output_zip": { "id": "a38ed44718641cdb", "src": "hda", "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/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, 1.96it/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, 1.96it/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": "2025-05-26T09:47:00.964337", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 4, "time_seconds": 34.59279441833496, "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": "09ac55ab9704eba2", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "dc7e3ab6a421767b", "src": "hdca" }, "genbank_files": { "id": "b1d9a1d43e36b679", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:47:41.246196", "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": "105127", "galaxy_version": "24.2", "handler": null, "history_id": "24f234959abeadac", "id": "271c0f8150c5b24a", "inputs": { "assembly_csv": { "id": "09ac55ab9704eba2", "src": "hda", "uuid": "0d80ec64-7c14-49ec-bf00-8b127413b402" }, "domesticated_input1": { "id": "f1e670d3230dc49d", "src": "hda", "uuid": "9073f5ed-6218-436e-9c90-40231a771418" }, "domesticated_input2": { "id": "d6d38b30a0e08779", "src": "hda", "uuid": "1c278033-6add-4e83-92ee-ece6b30d73b2" }, "domesticated_input3": { "id": "5df6658d98901785", "src": "hda", "uuid": "68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6" }, "domesticated_input4": { "id": "179c4c4e78c36c21", "src": "hda", "uuid": "e2abf373-3268-46a0-a6bd-889fe7061984" }, "domesticated_input5": { "id": "b1ed244e949762c6", "src": "hda", "uuid": "d71d0b7d-fc98-4d97-8a6b-e92bb229582e" }, "genbank_files1": { "id": "faf74795de9215e4", "src": "hda", "uuid": "bfe6c5a0-bee9-4fcd-bc48-1030fddae94b" }, "genbank_files2": { "id": "982fc2b45c634401", "src": "hda", "uuid": "5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb" }, "genbank_files3": { "id": "d49187f9d744460f", "src": "hda", "uuid": "b3ecd963-5e7a-4c86-91f3-8d8322471402" }, "genbank_files4": { "id": "271c0f8150c5b24a", "src": "hda", "uuid": "6f8d0b94-6f0f-470c-b36a-87256aa427c6" }, "genbank_files5": { "id": "954a11ecc737c99c", "src": "hda", "uuid": "2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e" }, "genbank_files6": { "id": "c90496f58e5d6dd9", "src": "hda", "uuid": "c5fde1d8-6078-4b1c-946d-fe58c868e1a5" }, "genbank_files7": { "id": "9c66fe6132ced54b", "src": "hda", "uuid": "0203ce08-8c98-4dcf-a274-ac69f126eb78" } }, "job_messages": [], "job_metrics": [], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "construct_gb": { "id": "7a37f3397bf88665", "src": "hdca" } }, "outputs": { "__new_primary_file_construct_gb|construct_1__": { "id": "ee6560cff5429b3a", "src": "hda", "uuid": "2d9d0878-8a8e-4a76-b4c7-8b2c58007a4c" }, "__new_primary_file_construct_gb|construct_2__": { "id": "7faeb5268234c1b7", "src": "hda", "uuid": "d8ead123-b416-446e-bcd7-12d88aa380d8" }, "__new_primary_file_construct_gb|construct_3__": { "id": "71b5e767ad5c3d19", "src": "hda", "uuid": "d3370005-e04e-41fe-91ca-5ae418062a9f" }, "__new_primary_file_construct_gb|construct_4__": { "id": "07cc2539cb83a207", "src": "hda", "uuid": "0a5f7883-f82b-4122-a882-76fadc52a358" }, "output_zip": { "id": "49de8d939dbbcfba", "src": "hda", "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/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, 2.41it/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, 2.41it/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": "2025-05-26T09:47:53.960080", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 5, "time_seconds": 52.97593927383423, "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": "e8ab24d23dab7d7f", "src": "hda" }, "assembly_plan_name": "Type2sRestrictionAssembly", "domesticated_input": { "id": "dfd75d2f0da631b2", "src": "hdca" }, "topology": "circular" }, "job": { "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": "2025-05-26T09:48:34.329479", "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": "106213", "galaxy_version": "24.2", "handler": null, "history_id": "67e443cb5516c0e0", "id": "07cc2539cb83a207", "inputs": { "assembly_csv": { "id": "e8ab24d23dab7d7f", "src": "hda", "uuid": "017ccfd4-4d46-44c1-99ad-af18724cfa9c" }, "domesticated_input1": { "id": "548eebef94e3a53d", "src": "hda", "uuid": "c26ad39f-1237-4c04-8f7f-73d2c5d9ad58" }, "domesticated_input10": { "id": "9e9d5c19538ef8ad", "src": "hda", 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"output_zip": { "id": "2ec06dcf804a9f1d", "src": "hda", "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/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, 2.41it/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, 2.41it/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": "2025-05-26T09:48:47.319875", "user_email": "planemo@galaxyproject.org", "user_id": "b5f519d254c4f536" }, "status": "success", "test_index": 6, "time_seconds": 53.241769552230835, "tool_id": "cloning_simulation", "tool_version": "0.1.0+galaxy0" }, "has_data": true, "id": "cloning_simulation-6" } ], "version": "0.1" }