INFO 2025-06-26 13:12:53,078 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 13:12:53,078 process.py process_mission():434 [1] dorado_info[mission]["comment"] = OCCO mission - Iridium not working - in conjunction with ESP deployments - ctdToUse = ctd1 INFO 2025-06-26 13:12:53,078 process.py process_mission():449 [1] Processing OCCO mission 2007.249.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:12:53,078 process.py download_process():165 [1] Download and processing steps for 2007.249.00 INFO 2025-06-26 13:12:53,078 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007249/2007.249.00 INFO 2025-06-26 13:12:53,079 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007249/2007.249.00 to /data/auv_data/dorado/missionlogs/2007.249.00 INFO 2025-06-26 13:12:59,750 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.249.00 INFO 2025-06-26 13:12:59,750 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/ctdDriver.log (23196667 bytes) INFO 2025-06-26 13:13:01,449 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.249.00/ctdDriver.log: [ 57 272 373 459 536 597 751 900 920 1179 1219 1295 1438 1449 1666 1701 1908 2201 2247 2279 2304 2742 3011 3288 3344 3457 3820 4088 4712 4714 5030 6302 6537 6538 7167 7667 7691 8013 8860 9393 10289 10706 11262 11374 11439 13353 14111 14755 15043 17078 17185 18322 18611 19450 20837 22190 22700 25508 27553 30417 30418 32960 33018 34275 36410 38433 41992 44215 44216 46790 48033 48768 49568 51447 54427 60119 60555 66894 67163 67859 68862 72452 74010 81125 87267 88236 90684 91112 91871 92366 94715 99199 102955 103458 107188 108045 108141 109569 114856 115545 118688 119923 123799 125997 127065 130549 135006 138955 141719 145551 146931 148433 152749 153051 155152 156867 160553 162719 163361 166482 168583 170175 175254 179736 180712 181118 182017 187611 188595 190564 194527 194942 195451 196614 202168 209173 211035 213065 215597 216285 219611 223400 223552 230514 231429 232285 236438 250573 255542 255894 256270 258699 259861 262834 263006] INFO 2025-06-26 13:13:01,517 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/ctdDriver2.log (23202293 bytes) INFO 2025-06-26 13:13:03,269 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.249.00/ctdDriver2.log: [ 2 350 451 537 615 676 980 998 1258 1298 1374 1562 1780 1988 2358 2383 2821 2833 3091 3365 3686 3897 4164 4349 4791 5107 5338 5492 6614 7242 7741 7764 8088 8834 8936 9468 10363 10780 11339 11452 13211 14186 14830 15119 16278 16441 17261 18685 19523 22263 25578 26333 27623 27767 30486 33028 33160 34342 37164 38497 42055 46850 48094 48829 48968 49627 54487 55599 55815 60181 60616 63101 67921 72511 74071 81355 87332 88302 90750 92432 93112 94781 97361 99265 103024 106452 107258 108116 108212 109639 114926 119992 123117 127133 130617 135074 139025 141789 145029 145207 145621 148504 152818 153803 155219 156933 160621 161938 162788 165325 168649 168862 175322 179804 180780 181186 182086 187680 188663 190631 192688 194594 195010 195519 196681 202231 208946 209237 215661 216512 219675 223464 223616 226198 226504 228134 230579 231494 232350 233180 236502 240354 250635 251922 255605 255957 259925 262898] INFO 2025-06-26 13:13:03,349 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/gps.log (195764 bytes) INFO 2025-06-26 13:13:03,379 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/hydroscatlog.log (15830054 bytes) INFO 2025-06-26 13:13:05,235 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.249.00/hydroscatlog.log: [ 3 4 5 20 22 23 30 84 88 102 173 230 328 637 662 715 776 824 842 843 850 897 933 935 946 948 1087 1107 1123 1368 1408 1484 1485 1629 1642 1665 1678 1860 1897 1999 2105 2188 2213 2390 2399 2446 2448 2449 2504 2611 2857 2956 3303 3533 3661 3814 4026 4355 4816 4909 4919 4922 5220 5239 5263 5472 5627 6048 6460 6515 7224 7376 7381 7784 7822 7882 7883 7907 8976 9078 9079 9612 9956 10154 10507 10924 10948 11483 11596 11662 12056 12159 12194 13359 13617 13847 14336 15269 16592 17412 17413 17425 18550 18839 19933 20212 21066 21067 22928 24587 25737 26388 26492 27782 27783 27926 30252 30647 33323 36640 37328 38661 39314 39772 40407 41222 42220 45778 45909 47017 47937 48261 49136 51674 51675 52895 54654 54905 55982 57174 60783 63268 67122 67392 68088 69101 72680 73402 73694 74239 74805 77545 80288 81355 81356 81523 83971 85777 87498 87499 88237 88470 90917 91345 92105 92601 93281 97469 99434 100222 100783 102694 103192 103696 106618 107425 108283 108380 114647 115092 115942 116919 117364 118924 120159 121812 123283 123284 124035 124036 125416 126232 126233 126983 127300 130785 131149 135240 137236 138260 140097 141957 145791 147169 148672 152487 152985 153876 153973 157102 160033 162954 163596 165492 166716 167034 168289 168817 168818 169031 170014 170410 173830 179786 180946 181352 181353 182251 183293 184474 186895 187428 188062 188829 188969 192854 194759 195684 196847 198295 199909 200834 202286 202397 202398 205796 206548 206802 209114 209405 216676 216677 216734 219840 223629 223781 226666 228297 230741 232512 232513 233342 234992 235088 235976 236599 236667 240519 242693 243303 250800 256120 256497 258734 258925 259199 259716 260089 262840 263234] INFO 2025-06-26 13:13:05,286 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/navigation.log (77702182 bytes) INFO 2025-06-26 13:13:10,995 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/isuslog.log (0 bytes) WARNING 2025-06-26 13:13:10,995 logs2netcdfs.py download_process_logs():790 [1] /data/auv_data/dorado/missionlogs/2007.249.00/isuslog.log is empty INFO 2025-06-26 13:13:10,996 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/parosci.log (27729926 bytes) INFO 2025-06-26 13:13:13,359 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/tailCone.log (3218491 bytes) INFO 2025-06-26 13:13:13,760 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.249.00/biolume.log (17955948 bytes) INFO 2025-06-26 13:13:15,471 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:13:16,394 logs2netcdfs.py download_process_logs():807 [1] Time to process: 16.64 seconds WARNING 2025-06-26 13:13:16,394 process.py download_process():196 [1] No lopc.bin file for 2007.249.00 INFO 2025-06-26 13:13:16,394 process.py calibrate():227 [1] Calibration steps for 2007.249.00 INFO 2025-06-26 13:13:16,837 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 13:13:16,839 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:13:17,447 calibrate.py _nudge_pos():1806 [1] 87: 0.160 -0.0000334 -0.0000277 88 0.30 -16.688 -17.282 2007-09-06T21:58:19.706521600 INFO 2025-06-26 13:13:17,539 calibrate.py _nudge_pos():1806 [1] 96: 0.160 -0.0000028 0.0000063 1799 6.13 -0.068 0.190 2007-09-06T22:04:35.710763520 INFO 2025-06-26 13:13:18,360 calibrate.py _nudge_pos():1806 [1] 174: 0.170 -0.0000850 -0.0004133 12263 41.21 -0.306 -1.858 2007-09-06T22:47:05.706076928 INFO 2025-06-26 13:13:19,096 calibrate.py _nudge_pos():1806 [1] 245: 0.190 0.0002226 -0.0005412 13115 43.83 0.753 -2.288 2007-09-06T23:32:05.701114624 INFO 2025-06-26 13:13:19,772 calibrate.py _nudge_pos():1806 [1] 310: 0.180 0.0001302 -0.0005078 11691 39.03 0.495 -2.411 2007-09-07T00:12:11.706291968 INFO 2025-06-26 13:13:20,475 calibrate.py _nudge_pos():1806 [1] 378: 0.190 -0.0007078 0.0000018 12239 40.86 -2.569 0.008 2007-09-07T00:54:11.703660288 INFO 2025-06-26 13:13:21,243 calibrate.py _nudge_pos():1806 [1] 449: 0.190 -0.0002807 -0.0004161 12172 40.63 -1.025 -1.897 2007-09-07T01:35:59.701850624 INFO 2025-06-26 13:13:21,277 calibrate.py _nudge_pos():1806 [1] 452: 0.190 0.0000061 0.0000099 139 0.46 1.960 3.994 2007-09-07T01:36:29.709795072 INFO 2025-06-26 13:13:22,278 calibrate.py _nudge_pos():1806 [1] 545: 0.200 0.0000748 -0.0002363 9579 31.96 0.347 -1.370 2007-09-07T02:09:59.702100992 INFO 2025-06-26 13:13:23,045 calibrate.py _nudge_pos():1806 [1] 617: 0.190 0.0000544 -0.0000595 2881 9.61 0.839 -1.146 2007-09-07T02:20:47.707709440 INFO 2025-06-26 13:13:23,891 calibrate.py _nudge_pos():1806 [1] 697: 0.200 -0.0003578 -0.0000540 11025 36.78 -1.442 -0.272 2007-09-07T02:58:53.701108480 INFO 2025-06-26 13:13:24,578 calibrate.py _nudge_pos():1806 [1] 761: 0.200 -0.0002659 0.0000080 6542 21.84 -1.805 0.068 2007-09-07T03:21:47.706982656 INFO 2025-06-26 13:13:25,340 calibrate.py _nudge_pos():1806 [1] 832: 0.200 -0.0000928 0.0000566 3514 11.73 -1.173 0.895 2007-09-07T03:34:41.703960064 INFO 2025-06-26 13:13:26,109 calibrate.py _nudge_pos():1806 [1] 904: 0.200 -0.0003348 0.0002787 13878 46.31 -1.072 1.115 2007-09-07T04:22:11.708721408 INFO 2025-06-26 13:13:26,154 calibrate.py _nudge_pos():1806 [1] 908: 0.010 -0.0000175 -0.0000024 150 0.50 -5.210 -0.892 2007-09-07T04:22:44.906447104 INFO 2025-06-26 13:13:26,992 calibrate.py _nudge_pos():1806 [1] 986: 0.010 -0.0001872 0.0003711 14914 49.76 -0.558 1.382 2007-09-07T05:13:47.906617344 INFO 2025-06-26 13:13:27,791 calibrate.py _nudge_pos():1806 [1] 1060: 0.020 -0.0001370 0.0005588 16977 56.65 -0.358 1.828 2007-09-07T06:11:39.908768768 INFO 2025-06-26 13:13:28,690 calibrate.py _nudge_pos():1806 [1] 1140: 0.020 -0.0002033 0.0005311 12829 42.81 -0.704 2.298 2007-09-07T06:55:47.907368448 INFO 2025-06-26 13:13:28,724 calibrate.py _nudge_pos():1806 [1] 1143: 0.030 0.0000209 0.0000176 135 0.45 6.941 7.314 2007-09-07T06:56:16.905381888 INFO 2025-06-26 13:13:29,540 calibrate.py _nudge_pos():1806 [1] 1216: 0.030 -0.0001224 0.0005299 12532 41.81 -0.434 2.348 2007-09-07T07:39:17.908571136 INFO 2025-06-26 13:13:30,382 calibrate.py _nudge_pos():1806 [1] 1292: 0.030 -0.0000615 0.0001570 4002 13.35 -0.683 2.180 2007-09-07T07:53:53.908560896 INFO 2025-06-26 13:13:30,416 calibrate.py _nudge_pos():1806 [1] 1295: 0.030 0.0000031 -0.0000072 105 0.35 1.337 -3.838 2007-09-07T07:54:16.906985472 INFO 2025-06-26 13:13:31,216 calibrate.py _nudge_pos():1806 [1] 1366: 0.040 0.0001276 -0.0000351 11703 39.05 0.484 -0.167 2007-09-07T08:34:29.901683968 INFO 2025-06-26 13:13:32,082 calibrate.py _nudge_pos():1806 [1] 1443: 0.040 0.0000512 -0.0000194 6033 20.13 0.377 -0.178 2007-09-07T08:55:53.903724032 INFO 2025-06-26 13:13:32,935 calibrate.py _nudge_pos():1806 [1] 1519: 0.050 0.0000494 -0.0000192 3458 11.55 0.633 -0.308 2007-09-07T09:08:41.901112576 INFO 2025-06-26 13:13:33,868 calibrate.py _nudge_pos():1806 [1] 1601: 0.040 0.0001353 -0.0003945 11669 38.95 0.515 -1.877 2007-09-07T09:48:59.905467904 INFO 2025-06-26 13:13:34,730 calibrate.py _nudge_pos():1806 [1] 1676: 0.050 0.0001484 -0.0001934 6881 22.96 0.957 -1.560 2007-09-07T10:13:11.905998848 INFO 2025-06-26 13:13:35,635 calibrate.py _nudge_pos():1806 [1] 1753: 0.050 0.0001085 -0.0002432 7051 23.53 0.683 -1.915 2007-09-07T10:37:59.904064256 INFO 2025-06-26 13:13:35,726 calibrate.py _nudge_pos():1806 [1] 1761: 0.050 -0.0000009 0.0000268 80 0.26 -0.522 18.874 2007-09-07T10:38:22.902488832 INFO 2025-06-26 13:13:36,602 calibrate.py _nudge_pos():1806 [1] 1838: 0.060 0.0001512 -0.0003090 9091 30.35 0.738 -1.887 2007-09-07T11:09:59.902535168 INFO 2025-06-26 13:13:37,390 calibrate.py _nudge_pos():1806 [1] 1908: 0.060 0.0002226 -0.0004319 12391 41.35 0.798 -1.936 2007-09-07T11:52:29.907847936 INFO 2025-06-26 13:13:38,291 calibrate.py _nudge_pos():1806 [1] 1988: 0.070 0.0001042 -0.0000854 3501 11.68 1.321 -1.354 2007-09-07T12:05:29.904414720 INFO 2025-06-26 13:13:38,315 calibrate.py _nudge_pos():1806 [1] 1990: 0.070 0.0000016 -0.0000070 170 0.56 0.416 -2.303 2007-09-07T12:06:04.902017024 INFO 2025-06-26 13:13:39,076 calibrate.py _nudge_pos():1806 [1] 2058: 0.070 0.0018150 0.0022426 14538 48.50 5.545 8.569 2007-09-07T12:55:41.908078080 INFO 2025-06-26 13:13:39,897 calibrate.py _nudge_pos():1806 [1] 2130: 0.080 0.0021782 0.0022250 13816 46.11 7.000 8.941 2007-09-07T13:42:59.903662080 INFO 2025-06-26 13:13:40,720 calibrate.py _nudge_pos():1806 [1] 2202: 0.080 0.0022412 0.0022813 14143 47.21 7.037 8.953 2007-09-07T14:31:23.904724480 INFO 2025-06-26 13:13:41,471 calibrate.py _nudge_pos():1806 [1] 2267: 0.090 0.0019211 0.0021071 13734 45.83 6.215 8.519 2007-09-07T15:18:17.901952512 INFO 2025-06-26 13:13:42,301 calibrate.py _nudge_pos():1806 [1] 2340: 0.090 0.0011802 0.0014907 10521 35.10 4.987 7.871 2007-09-07T15:54:35.902749184 INFO 2025-06-26 13:13:43,240 calibrate.py _nudge_pos():1806 [1] 2422: 0.090 0.0008457 0.0007106 4236 14.15 8.866 9.308 2007-09-07T16:10:05.909039360 INFO 2025-06-26 13:13:44,063 calibrate.py _nudge_pos():1806 [1] 2491: 0.090 0.0000826 0.0000504 409 1.36 8.990 6.853 2007-09-07T16:12:35.908763648 INFO 2025-06-26 13:13:44,087 calibrate.py _nudge_pos():1806 [1] 2493: 0.090 0.0000062 0.0000216 125 0.41 2.222 9.679 2007-09-07T16:13:01.906982656 INFO 2025-06-26 13:13:46,546 calibrate.py _nudge_pos():1862 [1] 2669: - - - 0 0.00 - - INFO 2025-06-26 13:13:46,546 calibrate.py _nudge_pos():1868 [1] Points in final series = 328989 WARNING 2025-06-26 13:13:46,983 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:14:19,940 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 5 of 263539 INFO 2025-06-26 13:14:21,966 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 0 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:14:40,642 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:14:42,574 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:14:42,578 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.249.00/ctd1.nc INFO 2025-06-26 13:14:42,579 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:14:42,580 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 13:14:42,580 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:14:56,987 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 21 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:14:58,939 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 21 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:14:58,943 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.249.00/ctd2.nc INFO 2025-06-26 13:14:58,945 calibrate.py _range_qc_combined_nc():898 [1] Setting 160 ctd2_salinity values to NaN INFO 2025-06-26 13:14:58,945 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 13:14:58,945 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 13:14:58,946 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.249.00 INFO 2025-06-26 13:14:58,995 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:15:02,091 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3945622 3945623 3945624] INFO 2025-06-26 13:15:02,680 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -8 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:15:02,688 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 13:15:02,688 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.249.00 ERROR 2025-06-26 13:15:02,689 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.249.00 INFO 2025-06-26 13:15:02,745 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_cal.nc INFO 2025-06-26 13:15:23,293 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 13:15:23,299 process.py align():251 [1] Alignment steps for 2007.249.00 INFO 2025-06-26 13:15:23,353 align.py process_cal():139 [1] Processing dorado_2007.249.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.249.00 INFO 2025-06-26 13:15:23,438 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:15:23,447 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:15:23,651 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:15:23,662 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:15:23,864 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:15:23,875 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:15:23,996 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:15:23,996 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:15:24,079 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:15:24,090 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:15:24,288 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:24,299 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:24,474 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:24,484 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:24,661 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:24,670 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:24,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:24,855 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:25,033 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:25,045 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:25,216 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:25,225 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:25,399 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:25,409 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:25,582 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:25,592 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:25,767 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:25,777 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:25,952 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:25,961 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:26,135 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:26,147 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:26,320 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:26,329 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:26,503 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:26,512 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:26,685 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:26,695 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:26,870 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:26,880 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:27,055 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:27,065 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:27,239 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:27,251 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:27,423 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:27,433 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:27,613 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:27,623 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:27,799 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.249.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:15:27,808 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:15:28,029 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:15:28,168 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 13:15:28,207 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_align.nc INFO 2025-06-26 13:15:28,338 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 13:15:28,340 process.py resample():273 [1] Resampling steps for 2007.249.00 INFO 2025-06-26 13:15:28,341 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:15:28,371 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_align.nc mission netCDF file INFO 2025-06-26 13:15:28,378 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_align.nc mission netCDF file INFO 2025-06-26 13:15:28,380 resample.py get_mission_start_end():1145 [1] navigation: 2007-09-06T21:57:14.211008256 to 2007-09-07T16:16:34.902391552 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 13:15:28,383 resample.py get_mission_start_end():1145 [1] hs2 : 2007-09-06T21:56:48.512768768 to 2007-09-07T16:16:35.062380544 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:15:28,386 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-09-06T21:57:30.229911040 to 2007-09-07T16:16:34.882392832 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 13:15:28,388 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-09-06T21:57:09.141355776 to 2007-09-07T16:16:34.912390656 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 13:15:28,390 resample.py get_mission_start_end():1145 [1] biolume : 2007-09-06T21:56:40.073312768 to 2007-09-07T16:16:33.802432512 (0 days 00:00:01.259948032 before mission_end) INFO 2025-06-26 13:15:28,391 resample.py get_mission_start_end():1145 [1] tailcone : 2007-09-06T21:56:44.123069440 to 2007-09-07T16:16:34.282434048 (0 days 00:00:00.779946496 before mission_end) INFO 2025-06-26 13:15:28,392 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_align.nc mission netCDF file INFO 2025-06-26 13:15:28,393 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,060 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,166 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,270 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,375 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,465 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,554 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,642 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,730 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,813 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,895 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:29,981 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,064 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,146 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,228 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,310 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,391 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,476 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,565 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,656 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,741 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,826 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,912 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,950 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:30,984 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:15:31,440 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_1S.nc INFO 2025-06-26 13:15:34,049 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:15:43,466 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.249.00/dorado_2007.249.00_1S_Gulper.txt INFO 2025-06-26 13:15:43,466 process.py archive():337 [1] Archiving steps for 2007.249.00 INFO 2025-06-26 13:15:43,466 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00, BASE_PATH = /data/auv_data INFO 2025-06-26 13:15:43,468 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:15:43,469 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.249.00_1S.nc INFO 2025-06-26 13:15:43,507 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:15:43,508 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.249.00_cal.nc INFO 2025-06-26 13:15:43,742 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:15:43,743 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.249.00_align.nc INFO 2025-06-26 13:15:43,952 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:15:44,018 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,084 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,090 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,136 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,334 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,413 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,428 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,595 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007249/2007.249.00 done. INFO 2025-06-26 13:15:44,596 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:15:44,597 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.249.00_1S_Gulper.txt INFO 2025-06-26 13:15:44,602 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.249.00/dorado_2007.249.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:15:44,602 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.249.00/dorado_2007.249.00_processing.log /Volumes/AUVCTD/surveys/2007/netcdf