--- a/output.json	Mon May 19 14:04:56 2025 +0000
+++ b/output.json	Fri May 23 09:04:43 2025 +0000
@@ -12,67 +12,67 @@
                     "adv|allow_edits": true,
                     "adv|use_file_names_as_ids": true,
                     "domestication_csv": {
-                        "id": "22ea85fb92532e6e",
+                        "id": "3f0c528bcd0d2af0",
                         "src": "hda"
                     },
                     "genbank_files": {
-                        "id": "fc7b6f0086a57c46",
+                        "id": "2d588720727ac897",
                         "src": "hdca"
                     },
                     "methylation_protection": false
                 },
                 "job": {
-                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpuknmm7vs/files/2/0/9/dataset_2091af2d-91c9-4b33-8247-8da805cbb225.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpuknmm7vs/files/1/3/7/dataset_137ae005-e411-4bef-9441-3ea8d396003f.dat,/tmp/tmpuknmm7vs/files/c/9/1/dataset_c911fc98-e598-4b2e-8986-84c7187c2213.dat,/tmp/tmpuknmm7vs/files/9/8/2/dataset_982f705a-0954-4779-a110-f7dbc98a61b5.dat,/tmp/tmpuknmm7vs/files/f/8/3/dataset_f83e35aa-c450-4d4d-97cd-9c825fd04b01.dat,/tmp/tmpuknmm7vs/files/1/b/1/dataset_1b16f72f-4138-41a9-a4fc-31ef4805f7a6.dat,/tmp/tmpuknmm7vs/files/a/3/7/dataset_a37dcf91-8835-452e-9af6-868f57e3f6ee.dat,/tmp/tmpuknmm7vs/files/e/5/a/dataset_e5a85113-f134-4446-abd1-12b8399a7fd6.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpuknmm7vs/files/1/3/7/dataset_137ae005-e411-4bef-9441-3ea8d396003f.dat:p3_2_CAG.gb,/tmp/tmpuknmm7vs/files/c/9/1/dataset_c911fc98-e598-4b2e-8986-84c7187c2213.dat:p7_gfp_sequence.gb,/tmp/tmpuknmm7vs/files/9/8/2/dataset_982f705a-0954-4779-a110-f7dbc98a61b5.dat:p14_CMVp.gb,/tmp/tmpuknmm7vs/files/f/8/3/dataset_f83e35aa-c450-4d4d-97cd-9c825fd04b01.dat:p16_bGHpolyA.gb,/tmp/tmpuknmm7vs/files/1/b/1/dataset_1b16f72f-4138-41a9-a4fc-31ef4805f7a6.dat:p18_CMVp.gb,/tmp/tmpuknmm7vs/files/a/3/7/dataset_a37dcf91-8835-452e-9af6-868f57e3f6ee.dat:p19_mNeoGreen.gb,/tmp/tmpuknmm7vs/files/e/5/a/dataset_e5a85113-f134-4446-abd1-12b8399a7fd6.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpuknmm7vs/job_working_directory/000/9/outputs/dataset_ae1aa491-d08a-4d37-a82c-ec44684acd17.dat'",
+                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/1/8/d/dataset_18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/f/3/b/dataset_f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/f/f/6/dataset_ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/8/c/d/dataset_8cd82e26-da60-4c91-bb80-d65d9ac0864d.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/a/f/6/dataset_af6f5158-3c00-4e30-a07f-b9cee1381d6c.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/b/9/7/dataset_b97d206b-3b81-41ad-96a6-462a3ebcbbf2.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/a/8/9/dataset_a8913c13-0cca-4e1e-9496-2c7f0bbcc485.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/6/c/c/dataset_6cc8ecc8-2001-4b71-8cd5-3d42f368a626.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/9/outputs/dataset_3847af4a-c6f8-4bc2-92e6-a5111f36e863.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-05-19T14:03:28.173560",
+                    "create_time": "2025-05-23T09:02:47.568318",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "260419",
+                    "external_id": "59522",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "fc7b6f0086a57c46",
-                    "id": "7756d22307ab703c",
+                    "history_id": "2d588720727ac897",
+                    "id": "05d1fab5f2f95c6e",
                     "inputs": {
                         "domestication_csv": {
-                            "id": "22ea85fb92532e6e",
+                            "id": "3f0c528bcd0d2af0",
                             "src": "hda",
-                            "uuid": "2091af2d-91c9-4b33-8247-8da805cbb225"
+                            "uuid": "18d1bdeb-a69c-4f9a-8d59-4d4d12fbff4c"
                         },
                         "genbank_files1": {
-                            "id": "fc7b6f0086a57c46",
+                            "id": "2d588720727ac897",
                             "src": "hda",
-                            "uuid": "137ae005-e411-4bef-9441-3ea8d396003f"
+                            "uuid": "f3b3d5cf-5f7f-4a6d-8c94-e7927144f3eb"
                         },
                         "genbank_files2": {
-                            "id": "b5d54d71116267fb",
+                            "id": "62972d51292f48e6",
                             "src": "hda",
-                            "uuid": "c911fc98-e598-4b2e-8986-84c7187c2213"
+                            "uuid": "ff62cd6f-ecf0-46ea-ac72-3cc78a217ef8"
                         },
                         "genbank_files3": {
-                            "id": "8e543ff561bc3697",
+                            "id": "e362c0fcc265e8f8",
                             "src": "hda",
-                            "uuid": "982f705a-0954-4779-a110-f7dbc98a61b5"
+                            "uuid": "8cd82e26-da60-4c91-bb80-d65d9ac0864d"
                         },
                         "genbank_files4": {
-                            "id": "ff69e25a80eeead0",
+                            "id": "9106613ee8ff8561",
                             "src": "hda",
-                            "uuid": "f83e35aa-c450-4d4d-97cd-9c825fd04b01"
+                            "uuid": "af6f5158-3c00-4e30-a07f-b9cee1381d6c"
                         },
                         "genbank_files5": {
-                            "id": "dbd8a678044720b3",
+                            "id": "0973ce805f0b9fc9",
                             "src": "hda",
-                            "uuid": "1b16f72f-4138-41a9-a4fc-31ef4805f7a6"
+                            "uuid": "b97d206b-3b81-41ad-96a6-462a3ebcbbf2"
                         },
                         "genbank_files6": {
-                            "id": "0723061c2449b3bc",
+                            "id": "3f7b9edb7f21ca84",
                             "src": "hda",
-                            "uuid": "a37dcf91-8835-452e-9af6-868f57e3f6ee"
+                            "uuid": "a8913c13-0cca-4e1e-9496-2c7f0bbcc485"
                         },
                         "genbank_files7": {
-                            "id": "3f340e0d71960888",
+                            "id": "898926e359e5028c",
                             "src": "hda",
-                            "uuid": "e5a85113-f134-4446-abd1-12b8399a7fd6"
+                            "uuid": "6cc8ecc8-2001-4b71-8cd5-3d42f368a626"
                         }
                     },
                     "job_messages": [],
@@ -83,56 +83,56 @@
                     "model_class": "Job",
                     "output_collections": {
                         "domesticated_gb": {
-                            "id": "b5d54d71116267fb",
+                            "id": "62972d51292f48e6",
                             "src": "hdca"
                         }
                     },
                     "outputs": {
                         "__new_primary_file_domesticated_gb|p14_CMVp__": {
-                            "id": "674b932f10cae6ec",
+                            "id": "0481fa54d30635c9",
                             "src": "hda",
-                            "uuid": "8428f6a9-247f-4276-9303-c15d412d77d8"
+                            "uuid": "a0555d82-443f-4b4b-8431-2a9d4e049017"
                         },
                         "__new_primary_file_domesticated_gb|p16_bGHpolyA__": {
-                            "id": "0d9edf3717cf870e",
+                            "id": "813bd8a24377d169",
                             "src": "hda",
-                            "uuid": "c9c4a7fd-4545-4aa0-a712-4219f7d46380"
+                            "uuid": "e506a4e3-7524-4360-abe1-b49ed99833d7"
                         },
                         "__new_primary_file_domesticated_gb|p18_CMVp__": {
-                            "id": "efc84d8a906cc770",
+                            "id": "d79d6af225946b08",
                             "src": "hda",
-                            "uuid": "a48975ae-b76f-408a-951a-bf5c00d48e5e"
+                            "uuid": "851cdd02-8f5a-400a-9b51-483c43d67028"
                         },
                         "__new_primary_file_domesticated_gb|p19_mNeoGreen__": {
-                            "id": "3ded7ccc765d3f3a",
+                            "id": "3ab85ee8e71bbdd5",
                             "src": "hda",
-                            "uuid": "366823c8-d7d0-4da8-b1be-cd735e794563"
+                            "uuid": "118d7f40-4850-466b-9f40-e360f1748011"
                         },
                         "__new_primary_file_domesticated_gb|p22_PGKpolyA__": {
-                            "id": "796ab0c34a0fb0fd",
+                            "id": "5480ebfe4604885a",
                             "src": "hda",
-                            "uuid": "5a67118d-1cb7-48d6-9d7a-e60a93550b59"
+                            "uuid": "b82fcc71-a34f-44f8-9dcf-546a10a5f2d6"
                         },
                         "__new_primary_file_domesticated_gb|p3_2_CAG__": {
-                            "id": "71039a18ff74d6c3",
+                            "id": "f174fd93dd20b3fc",
                             "src": "hda",
-                            "uuid": "1f4d81f9-3f4f-4ef8-b167-bbddb431660e"
+                            "uuid": "fa38ea29-3950-4e40-aed2-427b47597fc7"
                         },
                         "__new_primary_file_domesticated_gb|p7_gfp_sequence__": {
-                            "id": "765a087211afd1a5",
+                            "id": "58f99e5516a773cd",
                             "src": "hda",
-                            "uuid": "83ac3440-dff1-46c9-8685-dedcb799639a"
+                            "uuid": "538b66c4-b4d0-41b8-9355-afadc944621c"
                         },
                         "output_zip": {
-                            "id": "7756d22307ab703c",
+                            "id": "05d1fab5f2f95c6e",
                             "src": "hda",
-                            "uuid": "ae1aa491-d08a-4d37-a82c-ec44684acd17"
+                            "uuid": "3847af4a-c6f8-4bc2-92e6-a5111f36e863"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
                         "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
-                        "chromInfo": "\"/tmp/tmpuknmm7vs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "chromInfo": "\"/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                         "dbkey": "\"?\"",
                         "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
                         "methylation_protection": "false"
@@ -143,13 +143,13 @@
                     "tool_id": "domestication",
                     "tool_stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.75it/s, now=None]\r                                                               \r",
                     "tool_stdout": "Part names were not truncated\n",
-                    "update_time": "2025-05-19T14:03:39.118647",
+                    "update_time": "2025-05-23T09:02:58.973787",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "fc7b6f0086a57c46"
+                    "user_id": "2d588720727ac897"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 33.93032908439636,
+                "time_seconds": 34.70007658004761,
                 "tool_id": "domestication",
                 "tool_version": "0.1.0+galaxy1"
             },
@@ -162,20 +162,20 @@
                     "adv|allow_edits": true,
                     "adv|use_file_names_as_ids": true,
                     "domestication_csv": {
-                        "id": "1e850269971a1d95",
+                        "id": "0ac23d4d0b88827c",
                         "src": "hda"
                     },
                     "genbank_files": {
-                        "id": "8e543ff561bc3697",
+                        "id": "e362c0fcc265e8f8",
                         "src": "hdca"
                     },
                     "methylation_protection": true
                 },
                 "job": {
-                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpuknmm7vs/files/2/e/7/dataset_2e74abb7-8cbb-4fb8-bbd1-e6ade579fc0e.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpuknmm7vs/files/6/e/0/dataset_6e0e72b9-315b-4b6f-bf12-7173f9d50a6a.dat,/tmp/tmpuknmm7vs/files/3/8/e/dataset_38eb02ca-4588-496e-b2bf-c2d3f8dc4c08.dat,/tmp/tmpuknmm7vs/files/a/2/5/dataset_a25277e7-49b2-4735-893b-4bc686790d4b.dat,/tmp/tmpuknmm7vs/files/5/a/2/dataset_5a2f81c7-0187-4cde-aed1-a38f771d5774.dat,/tmp/tmpuknmm7vs/files/e/d/2/dataset_ed263438-ea3e-49eb-9ff5-63c168d74f73.dat,/tmp/tmpuknmm7vs/files/3/7/4/dataset_37446dea-30ab-4eda-9205-115e393987ef.dat,/tmp/tmpuknmm7vs/files/4/6/2/dataset_462c6f07-914c-49c8-8a95-9a2c55387b66.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpuknmm7vs/files/6/e/0/dataset_6e0e72b9-315b-4b6f-bf12-7173f9d50a6a.dat:p3_2_CAG.gb,/tmp/tmpuknmm7vs/files/3/8/e/dataset_38eb02ca-4588-496e-b2bf-c2d3f8dc4c08.dat:p7_gfp_sequence.gb,/tmp/tmpuknmm7vs/files/a/2/5/dataset_a25277e7-49b2-4735-893b-4bc686790d4b.dat:p14_CMVp.gb,/tmp/tmpuknmm7vs/files/5/a/2/dataset_5a2f81c7-0187-4cde-aed1-a38f771d5774.dat:p16_bGHpolyA.gb,/tmp/tmpuknmm7vs/files/e/d/2/dataset_ed263438-ea3e-49eb-9ff5-63c168d74f73.dat:p18_CMVp.gb,/tmp/tmpuknmm7vs/files/3/7/4/dataset_37446dea-30ab-4eda-9205-115e393987ef.dat:p19_mNeoGreen.gb,/tmp/tmpuknmm7vs/files/4/6/2/dataset_462c6f07-914c-49c8-8a95-9a2c55387b66.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpuknmm7vs/job_working_directory/000/18/outputs/dataset_bdb782f3-5124-4720-b76f-363142ea12eb.dat'",
+                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpa__rr6q2/files/8/9/c/dataset_89c41e63-3985-4c33-9154-735d98f3f2bb.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpa__rr6q2/files/3/7/a/dataset_37a61c0f-4043-404f-97c9-1b2e4b277a0b.dat:p3_2_CAG.gb,/tmp/tmpa__rr6q2/files/a/c/d/dataset_acd5b8cd-260a-4eed-bbaa-083097afd437.dat:p7_gfp_sequence.gb,/tmp/tmpa__rr6q2/files/b/4/2/dataset_b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd.dat:p14_CMVp.gb,/tmp/tmpa__rr6q2/files/6/4/3/dataset_643037ae-a752-4ce5-80e9-921fa8b24d3b.dat:p16_bGHpolyA.gb,/tmp/tmpa__rr6q2/files/d/c/e/dataset_dce00e9a-8b99-4bce-a1c2-b17377db99cf.dat:p18_CMVp.gb,/tmp/tmpa__rr6q2/files/0/2/0/dataset_020c2948-6eb0-4860-b17b-a3f35d138965.dat:p19_mNeoGreen.gb,/tmp/tmpa__rr6q2/files/2/c/6/dataset_2c6f9cf6-bf93-4c97-9ea8-17ad34702969.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpa__rr6q2/job_working_directory/000/18/outputs/dataset_257e63c3-87b5-459a-b118-921e6217abe8.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-05-19T14:04:01.809480",
+                    "create_time": "2025-05-23T09:03:22.156202",
                     "dependencies": [
                         {
                             "cacheable": false,
@@ -377,51 +377,51 @@
                         }
                     ],
                     "exit_code": 0,
-                    "external_id": "261147",
+                    "external_id": "60268",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "b5d54d71116267fb",
-                    "id": "98ddc29ec4b65d8b",
+                    "history_id": "62972d51292f48e6",
+                    "id": "e08d37863731003c",
                     "inputs": {
                         "domestication_csv": {
-                            "id": "1e850269971a1d95",
+                            "id": "0ac23d4d0b88827c",
                             "src": "hda",
-                            "uuid": "2e74abb7-8cbb-4fb8-bbd1-e6ade579fc0e"
+                            "uuid": "89c41e63-3985-4c33-9154-735d98f3f2bb"
                         },
                         "genbank_files1": {
-                            "id": "55d04483f52e4ac3",
+                            "id": "55d915b26d3a354e",
                             "src": "hda",
-                            "uuid": "6e0e72b9-315b-4b6f-bf12-7173f9d50a6a"
+                            "uuid": "37a61c0f-4043-404f-97c9-1b2e4b277a0b"
                         },
                         "genbank_files2": {
-                            "id": "98ddc29ec4b65d8b",
+                            "id": "e08d37863731003c",
                             "src": "hda",
-                            "uuid": "38eb02ca-4588-496e-b2bf-c2d3f8dc4c08"
+                            "uuid": "acd5b8cd-260a-4eed-bbaa-083097afd437"
                         },
                         "genbank_files3": {
-                            "id": "8d34910a63792da6",
+                            "id": "72fd2001a1c00c74",
                             "src": "hda",
-                            "uuid": "a25277e7-49b2-4735-893b-4bc686790d4b"
+                            "uuid": "b429cf4a-5fc0-4b2f-a27f-7b7d2da197dd"
                         },
                         "genbank_files4": {
-                            "id": "621625f9029b29e2",
+                            "id": "535975adfebcbd66",
                             "src": "hda",
-                            "uuid": "5a2f81c7-0187-4cde-aed1-a38f771d5774"
+                            "uuid": "643037ae-a752-4ce5-80e9-921fa8b24d3b"
                         },
                         "genbank_files5": {
-                            "id": "a0a7c91bd9b97c08",
+                            "id": "44c226435b38bb38",
                             "src": "hda",
-                            "uuid": "ed263438-ea3e-49eb-9ff5-63c168d74f73"
+                            "uuid": "dce00e9a-8b99-4bce-a1c2-b17377db99cf"
                         },
                         "genbank_files6": {
-                            "id": "0ee92de83756cc20",
+                            "id": "bbe178e57c4f8c81",
                             "src": "hda",
-                            "uuid": "37446dea-30ab-4eda-9205-115e393987ef"
+                            "uuid": "020c2948-6eb0-4860-b17b-a3f35d138965"
                         },
                         "genbank_files7": {
-                            "id": "1017e10ba43f3200",
+                            "id": "11bdfc4549627602",
                             "src": "hda",
-                            "uuid": "462c6f07-914c-49c8-8a95-9a2c55387b66"
+                            "uuid": "2c6f9cf6-bf93-4c97-9ea8-17ad34702969"
                         }
                     },
                     "job_messages": [],
@@ -432,73 +432,73 @@
                     "model_class": "Job",
                     "output_collections": {
                         "methprot_gb": {
-                            "id": "ff69e25a80eeead0",
+                            "id": "9106613ee8ff8561",
                             "src": "hdca"
                         }
                     },
                     "outputs": {
                         "__new_primary_file_methprot_gb|p14_CMVp__": {
-                            "id": "4ab3dc6df9d6ead7",
+                            "id": "63657e65b797e156",
                             "src": "hda",
-                            "uuid": "0d6ada79-a292-41ef-bb48-2c3a1ced45fa"
+                            "uuid": "ff3d4f80-e86b-4391-b395-1f11f74883e0"
                         },
                         "__new_primary_file_methprot_gb|p16_bGHpolyA__": {
-                            "id": "d6a092eaabdcc230",
+                            "id": "7000d26bf45ffb00",
                             "src": "hda",
-                            "uuid": "0977791c-edca-43cf-a704-f5da967621fa"
+                            "uuid": "0ea8ad54-9cee-4a88-9352-cbf201923fb8"
                         },
                         "__new_primary_file_methprot_gb|p18_CMVp__": {
-                            "id": "1d8417714248f578",
+                            "id": "36313fb553e6e307",
                             "src": "hda",
-                            "uuid": "8ee7ab25-5689-40e0-9a2b-0714514deb05"
+                            "uuid": "e6a1e8a2-1881-4ea9-9e2f-c2bc40a273a6"
                         },
                         "__new_primary_file_methprot_gb|p19_mNeoGreen__": {
-                            "id": "cb4ee5d51bedaa0c",
+                            "id": "12401c2b6811fee0",
                             "src": "hda",
-                            "uuid": "ad7062ff-f20b-472d-b7e4-8d39b5139f36"
+                            "uuid": "a73b7443-df14-4dea-84f3-381db57cca18"
                         },
                         "__new_primary_file_methprot_gb|p22_PGKpolyA__": {
-                            "id": "dfd900e887fa8515",
+                            "id": "0eb41dc2e09a8361",
                             "src": "hda",
-                            "uuid": "5740b96d-15a6-482b-ac23-a7f33444d5e7"
+                            "uuid": "67791634-ccbb-4984-82b6-5f6dabf17fd3"
                         },
                         "__new_primary_file_methprot_gb|p3_2_CAG__": {
-                            "id": "5ff13a8fc7f068b0",
+                            "id": "963b9ee6a9b85043",
                             "src": "hda",
-                            "uuid": "79a94038-ff98-4840-a766-7b92e9024f6b"
+                            "uuid": "a79b48fa-4414-4de6-9747-be228b0650ff"
                         },
                         "__new_primary_file_methprot_gb|p7_gfp_sequence__": {
-                            "id": "ace5ddee9ee23c8b",
+                            "id": "3716318b258c039e",
                             "src": "hda",
-                            "uuid": "e3f6ad6a-f19d-4edf-9eba-75ccf474d75f"
+                            "uuid": "3834e7e4-4365-4020-88d7-554281f0836f"
                         },
                         "output_zip": {
-                            "id": "ba419d6c663f507f",
+                            "id": "c2e357d169213b81",
                             "src": "hda",
-                            "uuid": "bdb782f3-5124-4720-b76f-363142ea12eb"
+                            "uuid": "257e63c3-87b5-459a-b118-921e6217abe8"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
                         "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
-                        "chromInfo": "\"/tmp/tmpuknmm7vs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "chromInfo": "\"/tmp/tmpa__rr6q2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                         "dbkey": "\"?\"",
                         "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
                         "methylation_protection": "true"
                     },
                     "state": "ok",
-                    "stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.74it/s, now=None]\r                                                               \r",
+                    "stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.73it/s, now=None]\r                                                               \r",
                     "stdout": "Part names were not truncated\n",
                     "tool_id": "domestication",
-                    "tool_stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.74it/s, now=None]\r                                                               \r",
+                    "tool_stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.73it/s, now=None]\r                                                               \r",
                     "tool_stdout": "Part names were not truncated\n",
-                    "update_time": "2025-05-19T14:04:12.722130",
+                    "update_time": "2025-05-23T09:03:33.301866",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "fc7b6f0086a57c46"
+                    "user_id": "2d588720727ac897"
                 },
                 "status": "success",
                 "test_index": 1,
-                "time_seconds": 33.47424507141113,
+                "time_seconds": 34.21326494216919,
                 "tool_id": "domestication",
                 "tool_version": "0.1.0+galaxy1"
             },