INFO 2025-06-26 23:23:00,145 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2015 --end_year 2025 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 23:23:00,145 process.py process_mission():434 [1] dorado_info[mission]["comment"] = December Dorado run with 60 cartridge ESP in the water QC note: Best CTD is ctd2, ctd2 not great but better for salt although a couple screwey profiles in temp, Nearly all salinity is bad - ctdToUse = ctd1 INFO 2025-06-26 23:23:00,145 process.py process_mission():449 [1] Processing Monterey Bay Diamond mission 2017.347.00 by user docker_user on host 355841a7028c INFO 2025-06-26 23:23:00,145 process.py download_process():165 [1] Download and processing steps for 2017.347.00 INFO 2025-06-26 23:23:00,145 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2017/2017347/2017.347.00 INFO 2025-06-26 23:23:00,145 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2017/2017347/2017.347.00 to /data/auv_data/dorado/missionlogs/2017.347.00 INFO 2025-06-26 23:23:05,238 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2017.347.00 INFO 2025-06-26 23:23:05,238 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/ctdDriver.log (19001478 bytes) INFO 2025-06-26 23:23:06,824 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/ctdDriver2.log (19011359 bytes) INFO 2025-06-26 23:23:08,371 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/gps.log (350492 bytes) INFO 2025-06-26 23:23:08,420 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/hydroscatlog.log (16662682 bytes) INFO 2025-06-26 23:23:10,260 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2017.347.00/hydroscatlog.log: [ 818 904 1084 2257 2995 3446 4633 5101 5533 5906 6734 6801 7289 7407 7511 8278 8285 8734 9134 9232 9864 9894 9914 10004 10337 10357 10624 12348 12924 13143 13144 13928 13936 13982 14009 14385 14464 14498 14768 14867 15347 16295 16418 17674 18061 18681 18957 19362 20224 21048 21313 21509 23154 23388 23801 24175 25311 25761 27197 27241 28187 28418 28841 29648 30695 30904 31144 31228 31789 32253 32479 32764 32994 33401 33949 34063 34207 34413 34656 35125 35511 36685 36751 37295 37372 37551 38233 38406 39142 39527 39888 39914 40063 40537 41112 41698 41731 43161 44443 44499 44539 45173 45179 45455 47199 47641 47855 48085 48153 48211 49302 49713 50033 50278 50765 50835 51954 52454 52862 53182 53201 53747 55397 56777 57255 57793 58781 59323 61177 61382 61387 61404 62918 63025 63041 63134 63537 64095 64242 65505 65706 66115 66495 67094 69056 69171 70197 71004 71291 71466 71947 72529 72706 73402 75007 75969 76911 77241 79002 79057 80952 81695 81805 82321 83108 83202 83473 83786 84116 85056 85275 86595 86904 87582 87760 87895 89068 89118 89193 89627 89630 90284 90325 90367 90872 91322 91703 91743 92047 92418 92492 93534 93842 94106 94837 94918 95556 95946 96240 96890 97238 97619 98478 101440 102227 102353 102699 102722 102730 104517 104546 105052 105122 105282 105330 105740 105766 106000 106190 106402 106866 106983 107023 107404 107416 107848 107879 108613 108844 108997 109972 110229 110626 111100 111616 111858 112105 112460 112726 112746 113059 113239 113432 114447 114794 115003 115134 115217 115299 115526 115987 116552 116634 116869 117132 117360 117785 117957 118996 119727 119774 120274 120307 120980 121410 121852 121941 124314 124756 124884 125039 125055 128690 128700 128829 129452 129618 129872 130099 130265 130544 130875 131266 131662 131736 131955 132140 132279 134241 134806 135605 137128 137262 137421 138224 138277 138850 138884 139587 139882 140230 140894 140951 141431 142255 142335 142830 143351 143877 143984 144294 144468 144472 144634 145278 145332 145567 145622 146627 146946 147287 147406 147424 147446 147507 149309 149681 152537 152907 154278 154451 154782 154938 156487 156806 157215 157337 157838 158479 158491 158830 158905 160481 160858 161483 161646 163040 163427 163821 164810 165255 165566 165578 165707 166053 166146 166347 167078 167450 167492 167529 167733 168898 168925 169852 170457 171489 171506 171586 171776 172153 172708 173972 174531 176250 177352 177368 179242 179431 179506 179851 180428 180437 180689 180926 182069 182835 183105 183913 184479 184747 185916 186589 186798 187025 187371 188551 188593 188806 188890 189115 189228 189273 189955 190331 190492 190758 191095 191630 191937 192438 193242 194200 195039 195202 195765 196079 197240 197270 197322 198300] INFO 2025-06-26 23:23:10,349 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/navigation.log (73383350 bytes) INFO 2025-06-26 23:23:16,447 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/isuslog.log (1235253 bytes) INFO 2025-06-26 23:23:16,585 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/parosci.log (23357798 bytes) INFO 2025-06-26 23:23:18,644 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2017.347.00/parosci.log: [79874] INFO 2025-06-26 23:23:18,750 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/tailCone.log (11908315 bytes) INFO 2025-06-26 23:23:20,384 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/biolume.log (13856498 bytes) INFO 2025-06-26 23:23:21,820 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 23:23:22,507 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2017.347.00/biolume.log: [10017 34223 36803 40718] INFO 2025-06-26 23:23:22,582 logs2netcdfs.py download_process_logs():807 [1] Time to process: 17.34 seconds INFO 2025-06-26 23:23:22,583 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2017.347.00/lopc.bin (34334332 bytes) INFO 2025-06-26 23:23:22,583 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 23:23:22 2025 INFO 2025-06-26 23:23:22,583 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2017.347.00/parosci.nc INFO 2025-06-26 23:23:22,583 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 23:23:22,583 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2017.347.00/parosci.nc INFO 2025-06-26 23:23:22,587 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1513205163.5, sensor_off_time = 1513254777.5 INFO 2025-06-26 23:23:22,588 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 49614 seconds. Expecting to read 99228 L frames from the lopc.bin file. INFO 2025-06-26 23:23:22,588 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 99228 records from the lopc.bin file. INFO 2025-06-26 23:23:23,172 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2017-12-13 22:46:03 Z and endTime = 2017-12-14 12:32:57 Z with 99228 records expected to be read from lopc.bin INFO 2025-06-26 23:23:23,173 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2017.347.00/lopc.bin INFO 2025-06-26 23:23:23,173 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2017.347.00/lopc.nc INFO 2025-06-26 23:23:23,173 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2017.347.00/lopc.nc INFO 2025-06-26 23:23:23,174 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2017.347.00 INFO 2025-06-26 23:23:23,174 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 23:23:23,232 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 23:23:23,232 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 23:23:23,232 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 23:23:28,181 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10000 11562 0 0 0 0 0 5.0 seconds, last L Frame: 99228 INFO 2025-06-26 23:23:32,666 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 20000 20453 0 0 0 0 0 4.5 seconds, last L Frame: 99228 INFO 2025-06-26 23:23:36,306 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 30000 26606 0 0 0 0 0 3.6 seconds, last L Frame: 99228 INFO 2025-06-26 23:23:39,829 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 40000 32376 0 0 0 0 0 3.5 seconds, last L Frame: 99228 ERROR 2025-06-26 23:23:43,195 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 23:23:43,198 process.py calibrate():227 [1] Calibration steps for 2017.347.00 INFO 2025-06-26 23:23:43,578 calibrate.py _navigation_process():1637 [1] Removing points outside of Monterey Bay for 2017.347.00/navigation.nc INFO 2025-06-26 23:23:43,580 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('navigation_latitude', Range(min=36, max=37)), ('navigation_longitude', Range(min=-122.1, max=-121.7))] INFO 2025-06-26 23:23:43,581 calibrate.py _range_qc_combined_nc():916 [1] navigation_time: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,595 calibrate.py _range_qc_combined_nc():916 [1] navigation_roll: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,599 calibrate.py _range_qc_combined_nc():916 [1] navigation_pitch: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,602 calibrate.py _range_qc_combined_nc():916 [1] navigation_yaw: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,606 calibrate.py _range_qc_combined_nc():916 [1] navigation_posx: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,610 calibrate.py _range_qc_combined_nc():916 [1] navigation_posy: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,613 calibrate.py _range_qc_combined_nc():916 [1] navigation_depth: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,616 calibrate.py _range_qc_combined_nc():916 [1] navigation_mWaterSpeed: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,620 calibrate.py _range_qc_combined_nc():916 [1] navigation_latitude: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,623 calibrate.py _range_qc_combined_nc():916 [1] navigation_longitude: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 23:23:43,634 calibrate.py _range_qc_combined_nc():936 [1] Done range checking navigation INFO 2025-06-26 23:23:43,638 calibrate.py _gps_process():2069 [1] Removing points outside of Monterey Bay for 2017.347.00/gps.nc INFO 2025-06-26 23:23:43,640 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('gps_latitude', Range(min=36, max=37)), ('gps_longitude', Range(min=-122.1, max=-121.7))] INFO 2025-06-26 23:23:43,640 calibrate.py _range_qc_combined_nc():916 [1] gps_time: deleting 1 values found outside of above ranges: ['2017-12-14T10:11:47.528652800'] INFO 2025-06-26 23:23:43,642 calibrate.py _range_qc_combined_nc():916 [1] gps_latitude: deleting 1 values found outside of above ranges: [55.7434725] INFO 2025-06-26 23:23:43,644 calibrate.py _range_qc_combined_nc():916 [1] gps_longitude: deleting 1 values found outside of above ranges: [-128.97650233] INFO 2025-06-26 23:23:43,648 calibrate.py _range_qc_combined_nc():936 [1] Done range checking gps INFO 2025-06-26 23:23:43,648 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 23:23:43,650 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 23:23:44,277 calibrate.py _nudge_pos():1806 [1] 92: 0.020 -0.0003907 -0.0000348 1670 5.56 -10.421 -1.161 2017-12-13T22:53:02.498508544 INFO 2025-06-26 23:23:46,036 calibrate.py _nudge_pos():1806 [1] 267: 0.040 0.0000137 0.0000046 20 0.06 32.105 13.603 2017-12-13T22:56:01.496246272 INFO 2025-06-26 23:23:46,155 calibrate.py _nudge_pos():1806 [1] 279: 0.140 -0.0018789 0.0022316 7060 23.53 -11.848 17.574 2017-12-13T23:19:44.498764032 INFO 2025-06-26 23:23:47,863 calibrate.py _nudge_pos():1806 [1] 445: 0.180 -0.0007414 -0.0008502 15406 51.35 -2.143 -3.068 2017-12-14T00:13:50.696384256 INFO 2025-06-26 23:23:50,235 calibrate.py _nudge_pos():1806 [1] 675: 0.120 -0.0000127 -0.0000428 8966 29.88 -0.063 -0.266 2017-12-14T00:47:32.897854208 INFO 2025-06-26 23:23:52,525 calibrate.py _nudge_pos():1806 [1] 896: 0.060 -0.0001186 -0.0000612 8951 29.83 -0.591 -0.380 2017-12-14T01:21:03.100145664 INFO 2025-06-26 23:23:54,583 calibrate.py _nudge_pos():1806 [1] 1096: 0.080 0.0000137 -0.0000417 35 0.11 17.920 -68.152 2017-12-14T01:24:29.096034048 INFO 2025-06-26 23:23:55,288 calibrate.py _nudge_pos():1806 [1] 1163: 0.020 -0.0004392 0.0000571 9591 31.97 -2.041 0.331 2017-12-14T01:57:33.300106752 INFO 2025-06-26 23:23:57,524 calibrate.py _nudge_pos():1806 [1] 1381: 0.170 -0.0004446 0.0000846 9085 30.28 -2.182 0.518 2017-12-14T02:31:32.300425472 INFO 2025-06-26 23:23:58,529 calibrate.py _nudge_pos():1806 [1] 1477: 0.170 -0.0000054 -0.0000180 15 0.05 -17.265 -71.301 2017-12-14T02:33:11.303643392 INFO 2025-06-26 23:23:58,877 calibrate.py _nudge_pos():1806 [1] 1511: 0.180 0.0000084 0.0000011 15 0.05 26.899 4.221 2017-12-14T02:33:48.301108736 INFO 2025-06-26 23:23:59,695 calibrate.py _nudge_pos():1806 [1] 1588: 0.040 0.0000581 0.0000544 16 0.05 172.692 201.509 2017-12-14T02:35:07.495683584 INFO 2025-06-26 23:23:59,813 calibrate.py _nudge_pos():1806 [1] 1599: 0.140 -0.0009833 0.0010341 10486 34.95 -4.182 5.483 2017-12-14T03:10:15.501275648 INFO 2025-06-26 23:24:02,254 calibrate.py _nudge_pos():1806 [1] 1831: 0.160 -0.0006269 -0.0003961 20 0.06 -1471.425 -1159.129 2017-12-14T03:14:10.495177216 INFO 2025-06-26 23:24:02,329 calibrate.py _nudge_pos():1806 [1] 1838: 0.130 0.0069641 0.0013301 12626 42.08 24.593 5.857 2017-12-14T03:56:21.701777664 INFO 2025-06-26 23:24:04,688 calibrate.py _nudge_pos():1806 [1] 2065: 0.150 -0.0001090 0.0000666 140 0.46 -34.950 26.640 2017-12-14T04:00:36.704308992 INFO 2025-06-26 23:24:04,741 calibrate.py _nudge_pos():1806 [1] 2070: 0.140 0.0101056 0.0037866 12921 43.07 34.863 16.292 2017-12-14T04:43:44.897005568 INFO 2025-06-26 23:24:05,083 calibrate.py _nudge_pos():1806 [1] 2101: 0.140 0.0101612 0.0037844 25 0.08 18872.532 8766.331 2017-12-14T04:44:21.904470528 INFO 2025-06-26 23:24:05,424 calibrate.py _nudge_pos():1806 [1] 2135: 0.150 0.0101635 0.0037771 40 0.13 11616.494 5384.200 2017-12-14T04:45:04.901524736 INFO 2025-06-26 23:24:05,539 calibrate.py _nudge_pos():1806 [1] 2146: 0.150 0.0101691 0.0037725 65 0.21 7082.685 3276.956 2017-12-14T04:45:27.899949312 INFO 2025-06-26 23:24:05,763 calibrate.py _nudge_pos():1806 [1] 2166: 0.150 -0.0000060 -0.0000012 50 0.16 -5.486 -1.389 2017-12-14T04:45:58.897826048 INFO 2025-06-26 23:24:05,775 calibrate.py _nudge_pos():1806 [1] 2167: 0.160 0.0000100 0.0000001 20 0.06 23.538 0.173 2017-12-14T04:46:02.897551872 INFO 2025-06-26 23:24:05,797 calibrate.py _nudge_pos():1806 [1] 2169: 0.160 -0.0000164 -0.0000014 15 0.05 -52.332 -5.623 2017-12-14T04:46:06.897277952 INFO 2025-06-26 23:24:05,870 calibrate.py _nudge_pos():1806 [1] 2176: 0.160 0.0000110 0.0000000 20 0.06 25.781 0.082 2017-12-14T04:46:17.896524544 INFO 2025-06-26 23:24:05,882 calibrate.py _nudge_pos():1806 [1] 2177: 0.160 -0.0000785 -0.0000029 75 0.25 -47.262 -2.185 2017-12-14T04:46:32.895496960 INFO 2025-06-26 23:24:07,647 calibrate.py _nudge_pos():1806 [1] 2342: 0.140 0.0091316 0.0049603 12056 40.18 33.756 22.874 2017-12-14T05:29:28.099083520 INFO 2025-06-26 23:24:09,839 calibrate.py _nudge_pos():1806 [1] 2550: 0.150 -0.0000681 -0.0002142 28 0.09 -112.378 -440.995 2017-12-14T05:33:03.104354304 INFO 2025-06-26 23:24:09,893 calibrate.py _nudge_pos():1806 [1] 2555: 0.130 0.0094419 0.0051701 12044 40.14 34.931 23.865 2017-12-14T06:13:16.299039488 INFO 2025-06-26 23:24:12,361 calibrate.py _nudge_pos():1806 [1] 2785: 0.140 0.0103035 0.0053633 13071 43.57 35.115 22.811 2017-12-14T07:00:40.504197888 INFO 2025-06-26 23:24:14,790 calibrate.py _nudge_pos():1806 [1] 3007: 0.110 0.0066385 0.0057266 10856 36.18 27.237 29.327 2017-12-14T07:40:33.700252672 INFO 2025-06-26 23:24:15,635 calibrate.py _nudge_pos():1806 [1] 3082: 0.100 0.0000446 0.0000379 20 0.06 104.229 110.464 2017-12-14T07:41:52.704840448 INFO 2025-06-26 23:24:17,285 calibrate.py _nudge_pos():1806 [1] 3233: 0.020 -0.0004754 0.0023359 6326 21.08 -3.347 20.530 2017-12-14T08:05:27.897893120 INFO 2025-06-26 23:24:17,326 calibrate.py _nudge_pos():1806 [1] 3236: 0.020 -0.0000894 -0.0000649 55 0.18 -73.708 -66.859 2017-12-14T08:05:40.897002752 INFO 2025-06-26 23:24:17,349 calibrate.py _nudge_pos():1806 [1] 3238: 0.020 0.0000152 -0.0000011 25 0.08 28.182 -2.580 2017-12-14T08:05:46.896591616 INFO 2025-06-26 23:24:17,360 calibrate.py _nudge_pos():1806 [1] 3239: 0.020 0.0000338 0.0000075 20 0.06 79.332 22.033 2017-12-14T08:05:50.896317696 INFO 2025-06-26 23:24:17,372 calibrate.py _nudge_pos():1806 [1] 3240: 0.030 0.0000524 0.0000272 20 0.06 122.886 79.612 2017-12-14T08:05:54.896043776 INFO 2025-06-26 23:24:17,404 calibrate.py _nudge_pos():1806 [1] 3243: 0.030 -0.0000485 -0.0000444 25 0.08 -89.936 -102.925 2017-12-14T08:06:01.895564032 INFO 2025-06-26 23:24:17,448 calibrate.py _nudge_pos():1806 [1] 3247: 0.030 0.0000758 0.0000317 15 0.05 241.180 125.859 2017-12-14T08:06:08.895084544 INFO 2025-06-26 23:24:17,470 calibrate.py _nudge_pos():1806 [1] 3249: 0.010 -0.0001486 -0.0001032 65 0.21 -103.316 -89.584 2017-12-14T08:06:22.904124928 INFO 2025-06-26 23:24:17,482 calibrate.py _nudge_pos():1806 [1] 3250: 0.020 -0.0000035 -0.0000266 20 0.06 -8.175 -77.696 2017-12-14T08:06:26.903851008 INFO 2025-06-26 23:24:17,503 calibrate.py _nudge_pos():1806 [1] 3252: 0.020 -0.0000725 -0.0000466 25 0.08 -134.471 -107.854 2017-12-14T08:06:33.903371520 INFO 2025-06-26 23:24:17,515 calibrate.py _nudge_pos():1806 [1] 3253: 0.020 0.0000377 0.0000067 25 0.08 70.025 15.627 2017-12-14T08:06:38.903028992 INFO 2025-06-26 23:24:17,537 calibrate.py _nudge_pos():1806 [1] 3255: 0.020 -0.0000599 -0.0000271 25 0.08 -111.137 -62.837 2017-12-14T08:06:44.902617856 INFO 2025-06-26 23:24:17,559 calibrate.py _nudge_pos():1806 [1] 3257: 0.030 -0.0000741 -0.0000444 30 0.10 -113.868 -85.100 2017-12-14T08:06:51.902138368 INFO 2025-06-26 23:24:17,571 calibrate.py _nudge_pos():1806 [1] 3258: 0.030 0.0000375 -0.0000169 145 0.48 11.586 -6.541 2017-12-14T08:07:20.900152064 INFO 2025-06-26 23:24:17,582 calibrate.py _nudge_pos():1806 [1] 3259: 0.030 0.0001418 0.0000652 40 0.13 161.950 92.942 2017-12-14T08:07:28.899603968 INFO 2025-06-26 23:24:17,594 calibrate.py _nudge_pos():1806 [1] 3260: 0.030 -0.0000887 -0.0000517 40 0.13 -101.303 -73.687 2017-12-14T08:07:36.899055872 INFO 2025-06-26 23:24:17,618 calibrate.py _nudge_pos():1806 [1] 3262: 0.030 0.0000461 0.0000192 20 0.06 107.992 56.182 2017-12-14T08:07:41.898713600 INFO 2025-06-26 23:24:17,742 calibrate.py _nudge_pos():1806 [1] 3272: 0.030 0.0000041 -0.0000114 15 0.05 12.904 -45.105 2017-12-14T08:07:55.897754368 INFO 2025-06-26 23:24:18,548 calibrate.py _nudge_pos():1806 [1] 3345: 0.030 0.0000095 -0.0000061 15 0.05 30.123 -24.376 2017-12-14T08:09:11.902547712 INFO 2025-06-26 23:24:18,635 calibrate.py _nudge_pos():1806 [1] 3353: 0.180 -0.0021683 0.0035296 10215 34.05 -9.452 19.210 2017-12-14T08:43:22.902044672 INFO 2025-06-26 23:24:21,341 calibrate.py _nudge_pos():1806 [1] 3594: 0.110 -0.0000155 0.0000088 144 0.48 -4.830 3.419 2017-12-14T08:47:51.903617024 INFO 2025-06-26 23:24:21,772 calibrate.py _nudge_pos():1806 [1] 3636: 0.160 -0.0044394 0.0038690 11545 38.48 -17.117 18.631 2017-12-14T09:26:59.102822656 INFO 2025-06-26 23:24:22,829 calibrate.py _nudge_pos():1806 [1] 3731: 0.040 -0.0000094 0.0000146 17 0.05 -26.190 50.772 2017-12-14T09:28:37.496082432 INFO 2025-06-26 23:24:23,626 calibrate.py _nudge_pos():1806 [1] 3803: 0.180 0.0000121 -0.0000336 25 0.08 22.375 -77.868 2017-12-14T09:29:54.100834560 INFO 2025-06-26 23:24:24,949 calibrate.py _nudge_pos():1806 [1] 3920: 0.160 -0.0060259 0.0027261 11991 39.97 -22.363 12.639 2017-12-14T10:11:49.298531840 INFO 2025-06-26 23:24:27,213 calibrate.py _nudge_pos():1806 [1] 4126: 0.030 -0.0000090 0.0000087 11 0.03 -39.918 48.463 2017-12-14T10:15:17.504268544 INFO 2025-06-26 23:24:27,361 calibrate.py _nudge_pos():1806 [1] 4139: 0.120 -0.0036325 0.0014234 10261 34.20 -15.750 7.712 2017-12-14T10:49:42.502806528 INFO 2025-06-26 23:24:29,902 calibrate.py _nudge_pos():1806 [1] 4366: 0.100 -0.0029421 0.0015736 10651 35.50 -12.286 8.214 2017-12-14T11:28:59.701327360 INFO 2025-06-26 23:24:32,277 calibrate.py _nudge_pos():1806 [1] 4593: 0.070 -0.0030973 0.0017117 10811 36.03 -12.738 8.802 2017-12-14T12:08:47.897724672 INFO 2025-06-26 23:24:34,625 calibrate.py _nudge_pos():1806 [1] 4818: 0.170 -0.0018294 0.0005196 5945 19.81 -13.681 4.860 2017-12-14T12:32:20.900927232 INFO 2025-06-26 23:24:35,003 calibrate.py _nudge_pos():1862 [1] 4814: - - - 3 0.01 - - INFO 2025-06-26 23:24:35,003 calibrate.py _nudge_pos():1868 [1] Points in final series = 247787 INFO 2025-06-26 23:25:07,631 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 80 of 197932 INFO 2025-06-26 23:25:09,111 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 23:25:11,018 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 23:25:12,455 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 23:25:12,459 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2017.347.00/ctd1.nc INFO 2025-06-26 23:25:12,460 calibrate.py _range_qc_combined_nc():898 [1] Setting 11 ctd1_salinity values to NaN INFO 2025-06-26 23:25:12,460 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 23:25:12,460 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 23:25:14,178 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 23:25:15,660 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 20 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 23:25:15,663 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2017.347.00/ctd2.nc WARNING 2025-06-26 23:25:15,668 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (185174) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 23:25:15,669 calibrate.py _range_qc_combined_nc():898 [1] Setting 185174 ctd2_salinity values to NaN INFO 2025-06-26 23:25:15,670 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 23:25:15,670 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 23:25:15,745 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 23:25:17,963 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 21660 21661 21662 ... 2904386 2904387 2904388] INFO 2025-06-26 23:25:18,388 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -7 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 23:26:05,000 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2017.347.00 ERROR 2025-06-26 23:26:05,000 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2017.347.00 INFO 2025-06-26 23:26:05,189 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_cal.nc INFO 2025-06-26 23:26:05,465 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_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 23:26:05,473 process.py align():251 [1] Alignment steps for 2017.347.00 INFO 2025-06-26 23:26:05,547 align.py process_cal():139 [1] Processing dorado_2017.347.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2017.347.00 INFO 2025-06-26 23:26:05,610 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 23:26:05,617 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 23:26:05,781 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 23:26:05,790 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 23:26:05,942 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 23:26:05,953 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 23:26:06,049 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 23:26:06,049 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 23:26:06,109 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 23:26:06,118 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 23:26:06,269 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:06,276 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:06,407 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:06,415 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:06,548 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:06,556 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:06,689 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:06,696 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:06,829 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:06,837 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:06,969 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:06,977 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,110 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,117 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,250 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,258 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,394 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,402 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,537 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,546 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,678 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,686 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,817 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,825 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:07,957 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:07,965 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,097 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,104 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,237 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,245 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,374 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,382 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,516 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,524 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,656 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,664 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,797 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,805 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:08,939 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:08,949 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:09,085 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:09,093 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:09,227 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2017.347.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 23:26:09,235 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 23:26:09,399 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 23:26:09,507 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 23:26:09,616 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 23:26:09,727 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 23:26:09,843 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 23:26:10,057 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.82 INFO 2025-06-26 23:26:11,287 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 23:26:11,390 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_align.nc INFO 2025-06-26 23:26:11,670 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_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 23:26:11,675 process.py resample():273 [1] Resampling steps for 2017.347.00 INFO 2025-06-26 23:26:11,676 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 23:26:11,742 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_align.nc mission netCDF file INFO 2025-06-26 23:26:11,750 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_align.nc mission netCDF file INFO 2025-06-26 23:26:11,752 resample.py get_mission_start_end():1145 [1] navigation: 2017-12-13T22:46:36.104978432 to 2017-12-14T12:32:57.498420224 (0 days 00:00:00 before mission_end) INFO 2025-06-26 23:26:11,754 resample.py get_mission_start_end():1145 [1] hs2 : 2017-12-13T22:46:02.417286144 to 2017-12-14T12:32:57.428424960 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 23:26:11,756 resample.py get_mission_start_end():1145 [1] ctd1 : 2017-12-13T22:46:39.874720000 to 2017-12-14T12:32:57.308433408 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 23:26:11,758 resample.py get_mission_start_end():1145 [1] ctd2 : 2017-12-13T22:46:23.545838592 to 2017-12-14T12:32:57.428424960 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 23:26:11,760 resample.py get_mission_start_end():1145 [1] isus : 2017-12-13T22:47:13.582411008 to 2017-12-14T12:32:56.498488576 (0 days 00:00:00.999931648 before mission_end) INFO 2025-06-26 23:26:11,761 resample.py get_mission_start_end():1145 [1] biolume : 2017-12-13T22:45:56.417662976 to 2017-12-14T12:32:56.098481920 (0 days 00:00:01.399938304 before mission_end) INFO 2025-06-26 23:26:11,763 resample.py get_mission_start_end():1145 [1] tailcone : 2017-12-13T22:46:01.647338752 to 2017-12-14T12:32:57.428424960 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 23:26:11,764 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_align.nc mission netCDF file INFO 2025-06-26 23:26:11,765 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,263 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,345 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,426 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,506 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,575 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,644 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,711 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,777 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,839 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,905 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:12,966 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,029 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,092 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,154 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,215 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,277 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,338 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,403 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,472 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,885 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:13,950 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,018 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,085 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,151 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,179 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,202 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,223 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,245 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,267 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:14,274 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 23:26:14,274 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 23:26:15,994 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 23:26:16,423 resample.py add_biolume_proxies():633 [1] Zero flow values found: 15 of 49621 - replaced with 350 ml/s INFO 2025-06-26 23:26:16,424 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 23:26:16,626 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 23:26:16,704 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 23:26:16,764 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 23:26:16,764 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 23:26:16,850 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 23:26:17,253 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_1S.nc INFO 2025-06-26 23:26:24,638 create_products.py _get_best_ctd():375 [1] Best CTD is ctd2 INFO 2025-06-26 23:26:53,771 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2017.347.00/dorado_2017.347.00_1S_Gulper.txt INFO 2025-06-26 23:26:53,771 process.py archive():337 [1] Archiving steps for 2017.347.00 INFO 2025-06-26 23:26:53,772 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00, BASE_PATH = /data/auv_data INFO 2025-06-26 23:26:53,773 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00 files to /Volumes/AUVCTD/surveys/2017/netcdf INFO 2025-06-26 23:26:53,774 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2017/netcdf/dorado_2017.347.00_1S.nc INFO 2025-06-26 23:26:53,820 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_1S.nc /Volumes/AUVCTD/surveys/2017/netcdf done. INFO 2025-06-26 23:26:53,821 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2017/netcdf/dorado_2017.347.00_cal.nc INFO 2025-06-26 23:26:54,114 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_cal.nc /Volumes/AUVCTD/surveys/2017/netcdf done. INFO 2025-06-26 23:26:54,115 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2017/netcdf/dorado_2017.347.00_align.nc INFO 2025-06-26 23:26:54,534 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_align.nc /Volumes/AUVCTD/surveys/2017/netcdf done. INFO 2025-06-26 23:26:54,591 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:54,642 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:54,649 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:54,691 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:54,879 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:54,892 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:54,960 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:55,003 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:55,141 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:55,224 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2017/2017347/2017.347.00 done. INFO 2025-06-26 23:26:55,225 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 23:26:55,227 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2017/odv/dorado_2017.347.00_1S_Gulper.txt INFO 2025-06-26 23:26:55,238 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2017.347.00/dorado_2017.347.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2017/odv done. INFO 2025-06-26 23:26:55,238 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2017.347.00/dorado_2017.347.00_processing.log /Volumes/AUVCTD/surveys/2017/netcdf