INFO 2025-06-26 11:49:23,199 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 11:49:23,199 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - as part of MB06 - Chavez survey for MB06 to fill in spots where glider's aren't going Had problem processing O2, no ISUS data (maybe some wierd bug whend there is no ISUS data) - ctdToUse = ctd1 INFO 2025-06-26 11:49:23,199 process.py process_mission():449 [1] Processing AUVCTD mission 2006.235.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:49:23,199 process.py download_process():165 [1] Download and processing steps for 2006.235.01 INFO 2025-06-26 11:49:23,199 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006235/2006.235.01 INFO 2025-06-26 11:49:23,199 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006235/2006.235.01 to /data/auv_data/dorado/missionlogs/2006.235.01 INFO 2025-06-26 11:49:30,222 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.235.01 INFO 2025-06-26 11:49:30,223 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/ctdDriver.log (26608779 bytes) INFO 2025-06-26 11:49:32,190 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.235.01/ctdDriver.log: [ 461 781 981 1001 2197 2230 2433 2687 3585 5263 6559 6745 7283 9029 12339 13752 23930 27341 59912 69835 70166 72319 87319 102999 103957 110604 124784 126900 129676 131492 131990 139774 154769 169766 173874 188454 192267 197865 208845 244762 252264 278742 280419 282258 282452] INFO 2025-06-26 11:49:32,270 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/ctdDriver2.log (26607893 bytes) INFO 2025-06-26 11:49:34,175 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.235.01/ctdDriver2.log: [ 609 743 995 1513 1840 2232 2646 3803 5451 5701 6549 7273 15856 20085 21742 22466 29886 31299 32074 34040 54641 68994 72314 99679 100623 110440 124774 131981 173863 188444 190242 194768 197854 199757 208400 208990 221019 222147 228877 244752 247459 252254 259750 278776 287762] INFO 2025-06-26 11:49:34,269 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/gps.log (334796 bytes) INFO 2025-06-26 11:49:34,313 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/hydroscatlog.log (18144134 bytes) INFO 2025-06-26 11:49:36,435 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.235.01/hydroscatlog.log: [ 44 102 852 1072 1326 1410 1614 1689 2224 3072 3329 5140 6222 6817 8306 9120 12093 12430 15898 16792 19937 20966 22984 25153 28912 31382 34154 34945 38494 45577 47425 60620 60826 64707 68183 80890 85728 94404 107045 109903 110707 116674 117749 127486 133751 139883 142867 152796 154188 162366 173964 174580 190334 192348 194857 198398 206680 207630 220747 229824 237317 244607 246033 251187 252263 252313 257360 261378 270493 276317 279609 280453 282290 290881] INFO 2025-06-26 11:49:36,494 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/navigation.log (89197034 bytes) INFO 2025-06-26 11:49:42,948 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/parosci.log (38874902 bytes) INFO 2025-06-26 11:49:46,141 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.235.01/parosci.log: [ 1 2 6 17 18 35 36 49 50 51 80 161 162 163 236 237 315 316 332 333 662 663 822 823 1381 2313 2747 2906 2907 3028 3808 4112 4283 4351 4552 5580 5883 5979 5981 6244 6245 6267 6268 6950 8244 8929 9232 9234 9255 9257 10633 11024 11025 11856 12252 13175 13346 13347 13774 13840 19749 19946 19947 21584 22235 22236 22786 22787 25792 25793 32357 34710 37035 40225 40763 42530 44917 44919 44920 45922 48528 48530 51716 51856 51857 53307 53313 53314 53986 56060 59693 59822 60366 64258 65125 67261 67262 77314 77776 77777 83881 84115 84520 84521 100786 100787 102930 121467 121468 121877 121937 121938 126098 133546 144299 144300 162683 162684 165157 165159 173071 179001 187069 187070 194377 194378 194379 208849 211462 213776 216366 229325 233834 235859 235860 240040 252539 252540 253883 253884 255544 260263 260264 263906 263907 273959 273960 284687 284688 288015 293167 293168 293179 309108 315100 329467 333560 337105 338149 338150 339732 339920 341201 341202 357068 369386 369387 374054 374450 381790 381791 381792 382473 383612 394541 394542 403643 406907 420964 420965 427301 427302 427303 431346 464690 470992 470994 475539 475540 480226 483722 484493 484494 484784 502792 502793 514683 514685 515107 521851 529106 529107 531333 534396 535197 540866 540867 540868 548496 548646 548647 559950 559951 569272 586066 586068 612506 615586 615587 617110 617111 635940 645755 655795 657825 657826 659070 663066 663068 689445 689446 707045 722880 724580 728464 728465 731391 733136 733137 746861 746862 751224 753823 753824 756654 756655 776827 776829 779114 797725 803273 807422 807423] INFO 2025-06-26 11:49:46,250 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/tailCone.log (18128827 bytes) INFO 2025-06-26 11:49:48,481 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.235.01/biolume.log (20578844 bytes) INFO 2025-06-26 11:49:50,429 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:49:51,486 logs2netcdfs.py download_process_logs():807 [1] Time to process: 21.26 seconds WARNING 2025-06-26 11:49:51,487 process.py download_process():196 [1] No lopc.bin file for 2006.235.01 INFO 2025-06-26 11:49:51,487 process.py calibrate():227 [1] Calibration steps for 2006.235.01 INFO 2025-06-26 11:49:52,063 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 11:49:52,066 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:49:52,480 calibrate.py _nudge_pos():1806 [1] 57: 0.020 0.0001347 0.0000249 25 0.08 248.709 57.638 2006-08-23T19:40:38.720421888 INFO 2025-06-26 11:49:52,652 calibrate.py _nudge_pos():1806 [1] 74: 0.030 -0.0011379 -0.0004014 5021 16.78 -10.014 -4.432 2006-08-23T19:57:41.720341504 INFO 2025-06-26 11:49:53,195 calibrate.py _nudge_pos():1806 [1] 127: 0.050 -0.0032879 0.0025076 15444 51.53 -9.425 9.017 2006-08-23T20:50:05.714962944 INFO 2025-06-26 11:49:53,991 calibrate.py _nudge_pos():1806 [1] 205: 0.040 0.0000311 -0.0000292 30 0.10 47.596 -55.994 2006-08-23T20:51:28.719276800 INFO 2025-06-26 11:49:54,763 calibrate.py _nudge_pos():1806 [1] 280: 0.030 -0.0000468 0.0000278 100 0.33 -20.952 15.611 2006-08-23T20:53:02.722837248 INFO 2025-06-26 11:49:54,785 calibrate.py _nudge_pos():1806 [1] 282: 0.040 -0.0000480 0.0000045 40 0.13 -54.496 6.442 2006-08-23T20:53:11.722220544 INFO 2025-06-26 11:49:54,816 calibrate.py _nudge_pos():1806 [1] 285: 0.040 -0.0001623 -0.0003420 15 0.05 -513.871 -1357.945 2006-08-23T20:53:16.721878016 INFO 2025-06-26 11:49:56,669 calibrate.py _nudge_pos():1806 [1] 468: 0.040 0.0000022 -0.0000112 15 0.05 6.875 -44.393 2006-08-23T20:56:21.719204864 INFO 2025-06-26 11:49:58,421 calibrate.py _nudge_pos():1806 [1] 639: 0.040 -0.0000224 0.0000037 15 0.05 -70.938 14.595 2006-08-23T20:59:14.717353728 INFO 2025-06-26 11:49:59,100 calibrate.py _nudge_pos():1806 [1] 706: 0.040 0.0000017 -0.0000152 15 0.05 5.339 -60.392 2006-08-23T21:00:23.722626560 INFO 2025-06-26 11:49:59,875 calibrate.py _nudge_pos():1806 [1] 781: 0.050 -0.0000141 -0.0000131 15 0.05 -44.543 -52.074 2006-08-23T21:01:40.717352192 INFO 2025-06-26 11:50:02,014 calibrate.py _nudge_pos():1806 [1] 989: 0.030 -0.0000118 0.0000057 15 0.05 -37.350 22.496 2006-08-23T21:05:11.722897408 INFO 2025-06-26 11:50:05,089 calibrate.py _nudge_pos():1806 [1] 1288: 0.040 0.0000131 -0.0000020 20 0.06 30.516 -5.738 2006-08-23T21:10:15.722071808 INFO 2025-06-26 11:50:05,748 calibrate.py _nudge_pos():1806 [1] 1353: 0.040 -0.0024974 0.0014372 9316 31.06 -11.878 8.573 2006-08-23T21:42:23.719995136 INFO 2025-06-26 11:50:06,578 calibrate.py _nudge_pos():1806 [1] 1434: 0.040 0.0000076 0.0000149 15 0.05 24.129 59.120 2006-08-23T21:43:46.714309376 INFO 2025-06-26 11:50:06,650 calibrate.py _nudge_pos():1806 [1] 1441: 0.040 -0.0000258 0.0000157 30 0.10 -39.444 30.164 2006-08-23T21:43:58.713487360 INFO 2025-06-26 11:50:08,723 calibrate.py _nudge_pos():1806 [1] 1643: 0.050 -0.0000417 0.0000056 50 0.16 -37.727 6.306 2006-08-23T21:47:29.719032576 INFO 2025-06-26 11:50:11,002 calibrate.py _nudge_pos():1806 [1] 1865: 0.050 -0.0000090 -0.0000024 20 0.06 -21.065 -7.142 2006-08-23T21:51:14.713619456 INFO 2025-06-26 11:50:13,069 calibrate.py _nudge_pos():1806 [1] 2067: 0.040 0.0000107 0.0000277 30 0.10 16.369 53.078 2006-08-23T21:54:41.719438592 INFO 2025-06-26 11:50:13,101 calibrate.py _nudge_pos():1806 [1] 2070: 0.040 -0.0000405 -0.0000365 45 0.15 -40.763 -46.178 2006-08-23T21:54:53.718616576 INFO 2025-06-26 11:50:13,122 calibrate.py _nudge_pos():1806 [1] 2072: 0.040 0.0000800 0.0000597 20 0.06 186.634 174.699 2006-08-23T21:54:58.718274048 INFO 2025-06-26 11:50:15,647 calibrate.py _nudge_pos():1806 [1] 2318: 0.050 -0.0026306 0.0018657 11975 39.93 -9.737 8.658 2006-08-23T22:38:59.717353216 INFO 2025-06-26 11:50:16,266 calibrate.py _nudge_pos():1806 [1] 2377: 0.060 -0.0033807 0.0025591 16806 56.03 -8.920 8.463 2006-08-23T23:35:59.713067520 INFO 2025-06-26 11:50:17,979 calibrate.py _nudge_pos():1806 [1] 2544: 0.050 -0.0000252 -0.0000265 15 0.05 -79.772 -105.185 2006-08-23T23:38:48.721489664 INFO 2025-06-26 11:50:17,991 calibrate.py _nudge_pos():1806 [1] 2545: 0.050 -0.0020834 0.0008602 8992 29.98 -10.275 5.317 2006-08-24T00:08:47.718249728 INFO 2025-06-26 11:50:18,856 calibrate.py _nudge_pos():1806 [1] 2627: 0.050 -0.0035598 -0.0022183 18463 61.55 -8.556 -6.679 2006-08-24T01:11:41.719713024 INFO 2025-06-26 11:50:19,275 calibrate.py _nudge_pos():1806 [1] 2667: 0.050 -0.0018735 -0.0020089 16511 55.05 -5.037 -6.762 2006-08-24T02:07:23.720770304 INFO 2025-06-26 11:50:19,844 calibrate.py _nudge_pos():1806 [1] 2719: 0.070 0.0010973 -0.0007397 8169 27.25 5.961 -5.030 2006-08-24T02:35:29.715271680 INFO 2025-06-26 11:50:20,279 calibrate.py _nudge_pos():1806 [1] 2759: 0.060 0.0024114 -0.0019741 13213 44.05 8.106 -8.305 2006-08-24T03:20:11.721541632 INFO 2025-06-26 11:50:20,688 calibrate.py _nudge_pos():1806 [1] 2797: 0.060 0.0059708 -0.0028442 15143 50.48 17.517 -10.440 2006-08-24T04:11:17.721506304 INFO 2025-06-26 11:50:21,195 calibrate.py _nudge_pos():1806 [1] 2845: 0.060 0.0050953 -0.0033055 14098 47.01 16.055 -13.028 2006-08-24T04:59:05.715035392 INFO 2025-06-26 11:50:21,684 calibrate.py _nudge_pos():1806 [1] 2891: 0.060 0.0055116 -0.0039988 13630 45.45 17.970 -16.304 2006-08-24T05:45:17.715140352 INFO 2025-06-26 11:50:22,194 calibrate.py _nudge_pos():1806 [1] 2939: 0.060 0.0053743 -0.0046789 13201 44.01 18.098 -19.699 2006-08-24T06:30:05.720999168 INFO 2025-06-26 11:50:22,738 calibrate.py _nudge_pos():1806 [1] 2990: 0.060 0.0052041 -0.0054330 13123 43.76 17.630 -23.004 2006-08-24T07:14:41.717680896 INFO 2025-06-26 11:50:23,309 calibrate.py _nudge_pos():1806 [1] 3043: 0.060 0.0049541 -0.0054281 12638 42.13 17.439 -23.874 2006-08-24T07:57:41.720938752 INFO 2025-06-26 11:50:23,879 calibrate.py _nudge_pos():1806 [1] 3095: 0.070 0.0051404 -0.0056667 12912 43.05 17.714 -24.393 2006-08-24T08:41:35.720497408 INFO 2025-06-26 11:50:24,442 calibrate.py _nudge_pos():1806 [1] 3146: 0.070 0.0040160 -0.0057265 12228 40.76 14.618 -26.031 2006-08-24T09:23:11.719509504 INFO 2025-06-26 11:50:25,060 calibrate.py _nudge_pos():1806 [1] 3200: 0.070 0.0004930 -0.0006623 2345 7.81 9.363 -15.707 2006-08-24T09:31:53.713750528 INFO 2025-06-26 11:50:25,580 calibrate.py _nudge_pos():1806 [1] 3248: 0.070 0.0038571 -0.0051150 13230 44.11 12.977 -21.486 2006-08-24T10:16:47.719198720 INFO 2025-06-26 11:50:26,250 calibrate.py _nudge_pos():1806 [1] 3308: 0.070 0.0024763 0.0002742 19591 65.31 5.625 0.778 2006-08-24T11:23:05.716687104 INFO 2025-06-26 11:50:26,970 calibrate.py _nudge_pos():1806 [1] 3371: 0.070 -0.0000506 0.0003466 16607 55.36 -0.136 1.160 2006-08-24T12:19:29.714867456 INFO 2025-06-26 11:50:27,539 calibrate.py _nudge_pos():1806 [1] 3422: 0.080 -0.0041142 0.0017086 18640 62.16 -9.813 5.093 2006-08-24T13:22:29.715919616 INFO 2025-06-26 11:50:28,316 calibrate.py _nudge_pos():1806 [1] 3486: 0.080 -0.0026062 0.0032621 15881 52.95 -7.296 11.416 2006-08-24T14:16:29.713964544 INFO 2025-06-26 11:50:30,706 calibrate.py _nudge_pos():1806 [1] 3693: 0.070 -0.0000418 -0.0000380 35 0.11 -54.663 -62.069 2006-08-24T14:20:02.719372544 INFO 2025-06-26 11:50:32,327 calibrate.py _nudge_pos():1806 [1] 3840: 0.070 0.0000259 -0.0000221 65 0.21 18.028 -19.185 2006-08-24T14:22:41.718480384 INFO 2025-06-26 11:50:32,950 calibrate.py _nudge_pos():1806 [1] 3896: 0.070 -0.0022611 0.0020167 13102 43.68 -7.671 8.555 2006-08-24T15:07:17.715162112 INFO 2025-06-26 11:50:33,843 calibrate.py _nudge_pos():1806 [1] 3974: 0.070 0.0000014 0.0000867 35 0.11 1.838 141.808 2006-08-24T15:08:42.719339008 INFO 2025-06-26 11:50:35,581 calibrate.py _nudge_pos():1806 [1] 4120: 0.070 -0.0000063 0.0000003 15 0.05 -20.147 1.379 2006-08-24T15:11:10.719200256 INFO 2025-06-26 11:50:36,967 calibrate.py _nudge_pos():1806 [1] 4245: 0.070 0.0000397 0.0000598 35 0.11 51.928 97.731 2006-08-24T15:13:21.720226048 INFO 2025-06-26 11:50:37,777 calibrate.py _nudge_pos():1806 [1] 4318: 0.080 -0.0010942 0.0011892 7059 23.53 -6.890 9.365 2006-08-24T15:38:05.718565120 INFO 2025-06-26 11:50:39,198 calibrate.py _nudge_pos():1806 [1] 4445: 0.070 -0.0015263 0.0012068 8127 27.10 -8.344 8.253 2006-08-24T16:07:17.718544896 INFO 2025-06-26 11:50:40,519 calibrate.py _nudge_pos():1806 [1] 4562: 0.080 0.0000090 -0.0000244 15 0.05 28.521 -97.064 2006-08-24T16:09:16.720392704 INFO 2025-06-26 11:50:41,238 calibrate.py _nudge_pos():1806 [1] 4626: 0.080 -0.0007489 -0.0004052 8929 29.76 -3.728 -2.523 2006-08-24T16:40:05.713728000 INFO 2025-06-26 11:50:41,370 calibrate.py _nudge_pos():1862 [1] 4615: - - - 3 0.01 - - INFO 2025-06-26 11:50:41,370 calibrate.py _nudge_pos():1868 [1] Points in final series = 377945 WARNING 2025-06-26 11:50:54,500 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:51:32,532 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 302313 INFO 2025-06-26 11:51:34,971 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:51:56,620 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:51:58,933 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:51:58,938 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.235.01/ctd1.nc INFO 2025-06-26 11:51:58,940 calibrate.py _range_qc_combined_nc():898 [1] Setting 72 ctd1_salinity values to NaN INFO 2025-06-26 11:51:58,940 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 11:51:58,940 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:52:15,737 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:52:18,005 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:52:18,010 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.235.01/ctd2.nc INFO 2025-06-26 11:52:18,012 calibrate.py _range_qc_combined_nc():898 [1] Setting 72 ctd2_salinity values to NaN INFO 2025-06-26 11:52:18,012 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 11:52:18,012 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 11:52:18,012 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.235.01 INFO 2025-06-26 11:52:18,069 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:52:21,670 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4505107 4505108 4505109] INFO 2025-06-26 11:52:22,485 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:52:22,491 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 11:52:22,494 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.235.01 ERROR 2025-06-26 11:52:22,494 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.235.01 INFO 2025-06-26 11:52:22,779 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_cal.nc INFO 2025-06-26 11:52:46,547 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 11:52:46,551 process.py align():251 [1] Alignment steps for 2006.235.01 INFO 2025-06-26 11:52:46,597 align.py process_cal():139 [1] Processing dorado_2006.235.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.235.01 INFO 2025-06-26 11:52:46,693 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:52:46,703 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:52:46,941 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:52:46,956 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:52:47,187 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:52:47,199 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:52:47,343 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:52:47,343 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:52:47,461 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:52:47,474 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:52:47,699 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:52:47,710 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:47,909 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:52:47,920 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:48,122 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:52:48,133 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:48,332 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:48,343 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:48,551 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:48,565 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:48,764 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:48,774 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:48,976 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:48,987 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:49,188 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:49,200 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:49,403 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:49,414 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:49,614 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:49,625 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:49,823 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:49,836 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:50,048 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:50,059 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:50,261 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:50,271 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:50,470 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:50,481 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:50,682 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:50,693 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:50,889 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:50,899 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:51,102 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:51,113 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:51,313 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:51,325 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:51,529 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:51,540 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:51,740 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.235.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:52:51,753 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:52:52,014 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:52:52,193 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 11:52:52,343 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_align.nc INFO 2025-06-26 11:52:52,507 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 11:52:52,509 process.py resample():273 [1] Resampling steps for 2006.235.01 INFO 2025-06-26 11:52:52,510 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:52:52,542 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_align.nc mission netCDF file INFO 2025-06-26 11:52:52,551 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_align.nc mission netCDF file INFO 2025-06-26 11:52:52,553 resample.py get_mission_start_end():1145 [1] navigation: 2006-08-23T19:40:01.432976128 to 2006-08-24T16:40:17.522918912 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 11:52:52,556 resample.py get_mission_start_end():1145 [1] hs2 : 2006-08-23T19:39:43.714189824 to 2006-08-24T16:40:17.532918528 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 11:52:52,559 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-08-23T19:40:07.842536960 to 2006-08-24T16:40:17.532918528 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 11:52:52,562 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-08-23T19:40:09.402429952 to 2006-08-24T16:40:17.622912256 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:52:52,564 resample.py get_mission_start_end():1145 [1] biolume : 2006-08-23T19:39:39.314456832 to 2006-08-24T16:40:16.792934912 (0 days 00:00:00.829977344 before mission_end) INFO 2025-06-26 11:52:52,567 resample.py get_mission_start_end():1145 [1] tailcone : 2006-08-23T19:39:40.144434432 to 2006-08-24T16:40:17.432925184 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 11:52:52,568 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_align.nc mission netCDF file INFO 2025-06-26 11:52:52,569 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:53,349 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:53,473 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:53,591 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:53,711 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:53,815 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:53,917 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,019 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,120 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,216 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,313 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,410 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,506 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,602 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,698 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,794 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,890 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:54,990 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,096 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,196 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,298 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,401 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,502 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,547 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:55,660 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:52:56,184 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_1S.nc INFO 2025-06-26 11:52:58,976 create_products.py gulper_odv():401 [1] No gulper times found for 2006.235.01 INFO 2025-06-26 11:52:58,976 process.py archive():337 [1] Archiving steps for 2006.235.01 INFO 2025-06-26 11:52:58,976 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01, BASE_PATH = /data/auv_data INFO 2025-06-26 11:52:58,978 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:52:58,979 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.235.01_1S.nc INFO 2025-06-26 11:52:59,029 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:52:59,030 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.235.01_cal.nc INFO 2025-06-26 11:52:59,317 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:52:59,318 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.235.01_align.nc INFO 2025-06-26 11:52:59,585 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:52:59,665 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:52:59,736 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:52:59,742 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:52:59,795 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:53:00,010 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:53:00,130 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:53:00,193 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:53:00,386 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006235/2006.235.01 done. INFO 2025-06-26 11:53:00,386 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:53:00,387 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.235.01/dorado_2006.235.01_processing.log /Volumes/AUVCTD/surveys/2006/netcdf