INFO 2025-06-26 11:41:30,505 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 11:41:30,505 process.py process_mission():434 [1] dorado_info[mission]["comment"] = BIOUME mission - as part of MB06 - Standard Haddock section (split out DAllanB iridium messages) - ctdToUse = ctd1 INFO 2025-06-26 11:41:30,505 process.py process_mission():449 [1] Processing BIOLUME mission 2006.227.08 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:41:30,505 process.py download_process():165 [1] Download and processing steps for 2006.227.08 INFO 2025-06-26 11:41:30,505 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006227/2006.227.08 INFO 2025-06-26 11:41:30,506 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006227/2006.227.08 to /data/auv_data/dorado/missionlogs/2006.227.08 INFO 2025-06-26 11:41:36,760 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.227.08 INFO 2025-06-26 11:41:36,760 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/ctdDriver.log (14538523 bytes) INFO 2025-06-26 11:41:37,903 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.08/ctdDriver.log: [ 6 2747 2810 5433 7975 28903 41068 55458 64668 137083 155010] INFO 2025-06-26 11:41:37,962 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/ctdDriver2.log (14537725 bytes) INFO 2025-06-26 11:41:39,142 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.08/ctdDriver2.log: [ 192 370 450 1785 2746 2809 5017 5431 7517 7973 9723 16900 25348 28899 41064 41243 44912 51522 77550 105765 109506 115318 117146 133336 137074 147139 157171 164467] INFO 2025-06-26 11:41:39,227 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/gps.log (80132 bytes) INFO 2025-06-26 11:41:39,248 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/hydroscatlog.log (9915434 bytes) INFO 2025-06-26 11:41:40,519 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.08/hydroscatlog.log: [ 3 354 509 843 2403 3874 4406 4601 5392 11094 18302 19773 33152 40660 61725 68350 82742 85757 106272 114959 142307 157155] INFO 2025-06-26 11:41:40,572 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/navigation.log (48735070 bytes) INFO 2025-06-26 11:41:44,952 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/isuslog.log (991189 bytes) INFO 2025-06-26 11:41:45,056 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/parosci.log (21210614 bytes) INFO 2025-06-26 11:41:46,942 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.227.08/parosci.log: [ 1 24 25 37 38 39 60 62 1410 1758 2003 2142 2286 2300 2747 2748 2896 2897 2898 2971 4286 4319 4560 4561 4570 4866 5013 5516 5890 6821 7960 7961 8804 9236 9237 9499 9500 10236 11668 12332 12343 13755 13756 15481 15490 17447 19268 30384 30402 31480 34538 37115 39030 45413 52906 55675 59537 73415 83494 85192 88696 92456 93034 101957 108931 110592 111739 112460 113097 121822 127184 127185 129609 130682 133147 138471 165141 165569 165723 165724 170876 193296 205661 205662 206587 206588 207717 208034 208035 221355 224669 233381 243666 253409 258256 260603 262660 262661 273432 273433 281656 283105 284253 295597 300658 301205 301206 301947 301948 303485 307476 307477 319655 335804 339796 339797 345637 350868 350869 376648 380430 380575 383851 389328 392108 392109 420262 420263 433019 433020] INFO 2025-06-26 11:41:47,037 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/tailCone.log (9905659 bytes) INFO 2025-06-26 11:41:48,356 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.227.08/biolume.log (11247340 bytes) INFO 2025-06-26 11:41:49,493 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:41:50,133 logs2netcdfs.py download_process_logs():807 [1] Time to process: 13.37 seconds WARNING 2025-06-26 11:41:50,134 process.py download_process():196 [1] No lopc.bin file for 2006.227.08 INFO 2025-06-26 11:41:50,134 process.py calibrate():227 [1] Calibration steps for 2006.227.08 INFO 2025-06-26 11:41:50,458 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 11:41:50,461 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:41:51,275 calibrate.py _nudge_pos():1806 [1] 97: 0.160 -0.0003011 -0.0001180 2192 7.33 -6.109 -2.983 2006-08-15T03:16:41.319250944 INFO 2025-06-26 11:41:51,765 calibrate.py _nudge_pos():1806 [1] 144: 0.160 -0.0019870 -0.0016500 5460 18.23 -16.207 -16.771 2006-08-15T03:35:41.321155584 INFO 2025-06-26 11:41:52,186 calibrate.py _nudge_pos():1806 [1] 184: 0.170 -0.0040210 -0.0029824 10150 33.85 -17.659 -16.327 2006-08-15T04:10:11.319351040 INFO 2025-06-26 11:41:52,591 calibrate.py _nudge_pos():1806 [1] 225: 0.170 -0.0042798 -0.0027956 9757 32.53 -19.551 -15.924 2006-08-15T04:43:23.322889216 INFO 2025-06-26 11:41:53,068 calibrate.py _nudge_pos():1806 [1] 269: 0.170 -0.0047370 -0.0030908 10794 35.98 -19.558 -15.918 2006-08-15T05:20:05.322042112 INFO 2025-06-26 11:41:53,460 calibrate.py _nudge_pos():1806 [1] 307: 0.190 -0.0040794 -0.0007762 9142 30.48 -19.876 -4.719 2006-08-15T05:51:11.324211968 INFO 2025-06-26 11:41:53,943 calibrate.py _nudge_pos():1806 [1] 351: 0.180 -0.0037618 -0.0006619 6951 23.18 -24.096 -5.291 2006-08-15T06:15:05.315976960 INFO 2025-06-26 11:41:54,393 calibrate.py _nudge_pos():1806 [1] 394: 0.180 -0.0015084 0.0000408 2550 8.50 -26.357 0.890 2006-08-15T06:24:17.318162176 INFO 2025-06-26 11:41:54,812 calibrate.py _nudge_pos():1806 [1] 435: 0.180 -0.0038068 0.0027667 8319 27.73 -20.375 18.488 2006-08-15T06:52:41.321430016 INFO 2025-06-26 11:41:55,277 calibrate.py _nudge_pos():1806 [1] 478: 0.180 -0.0028520 0.0024159 7019 23.40 -18.087 19.134 2006-08-15T07:16:47.322372096 INFO 2025-06-26 11:41:55,765 calibrate.py _nudge_pos():1806 [1] 522: 0.200 -0.0040461 0.0028534 9111 30.38 -19.755 17.404 2006-08-15T07:47:53.314543104 INFO 2025-06-26 11:41:56,210 calibrate.py _nudge_pos():1806 [1] 563: 0.190 -0.0040591 0.0030562 10388 34.63 -17.381 16.355 2006-08-15T08:23:11.319449600 INFO 2025-06-26 11:41:56,697 calibrate.py _nudge_pos():1806 [1] 609: 0.190 -0.0040334 0.0020985 9311 31.04 -19.258 12.526 2006-08-15T08:54:59.318742784 INFO 2025-06-26 11:41:57,181 calibrate.py _nudge_pos():1806 [1] 655: 0.020 -0.0044770 0.0019923 9524 31.75 -20.895 11.629 2006-08-15T09:27:29.515144960 INFO 2025-06-26 11:41:57,678 calibrate.py _nudge_pos():1806 [1] 701: 0.190 -0.0031401 0.0014984 7214 24.05 -19.344 11.547 2006-08-15T09:52:17.323223296 INFO 2025-06-26 11:41:58,142 calibrate.py _nudge_pos():1806 [1] 743: 0.010 -0.0005530 0.0005224 2404 8.01 -10.222 12.080 2006-08-15T10:00:59.517450496 INFO 2025-06-26 11:41:58,688 calibrate.py _nudge_pos():1806 [1] 793: 0.010 0.0000775 0.0003509 8034 26.78 0.429 2.428 2006-08-15T10:28:35.524006400 INFO 2025-06-26 11:41:59,179 calibrate.py _nudge_pos():1806 [1] 839: 0.010 0.0000020 0.0005693 8651 28.85 0.010 3.657 2006-08-15T10:58:11.522341888 INFO 2025-06-26 11:41:59,760 calibrate.py _nudge_pos():1806 [1] 890: 0.020 -0.0003758 -0.0000691 15557 51.86 -1.074 -0.247 2006-08-15T11:50:53.515730688 INFO 2025-06-26 11:42:00,297 calibrate.py _nudge_pos():1806 [1] 935: 0.020 -0.0007524 -0.0003946 13816 46.06 -2.421 -1.587 2006-08-15T12:37:41.523368960 INFO 2025-06-26 11:42:00,874 calibrate.py _nudge_pos():1806 [1] 985: 0.050 -0.0017770 -0.0007774 16701 55.68 -4.732 -2.587 2006-08-15T13:34:11.521138176 INFO 2025-06-26 11:42:01,388 calibrate.py _nudge_pos():1806 [1] 1031: 0.050 -0.0009406 -0.0004846 13212 44.05 -3.167 -2.039 2006-08-15T14:18:59.516997888 INFO 2025-06-26 11:42:01,904 calibrate.py _nudge_pos():1806 [1] 1077: 0.050 -0.0003670 -0.0001517 4963 16.55 -3.290 -1.699 2006-08-15T14:36:17.515890176 INFO 2025-06-26 11:42:02,161 calibrate.py _nudge_pos():1862 [1] 1079: - - - 5 0.01 - - INFO 2025-06-26 11:42:02,161 calibrate.py _nudge_pos():1868 [1] Points in final series = 206414 WARNING 2025-06-26 11:42:09,607 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:42:32,559 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:42:44,482 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:42:45,719 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:42:45,722 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.227.08/ctd1.nc INFO 2025-06-26 11:42:45,724 calibrate.py _range_qc_combined_nc():898 [1] Setting 142 ctd1_salinity values to NaN INFO 2025-06-26 11:42:45,724 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 11:42:45,724 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:42:54,984 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:42:56,206 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:42:56,209 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.227.08/ctd2.nc INFO 2025-06-26 11:42:56,211 calibrate.py _range_qc_combined_nc():898 [1] Setting 34 ctd2_salinity values to NaN INFO 2025-06-26 11:42:56,211 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 11:42:56,211 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:42:56,273 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:42:58,227 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 120 121 122 420 421 422 423 424 425 1380 1381 1382 1383 1384 1385 1860 7080 7081 7082 7083 7084 7085 7086 7087 7088 7320 7321 7322 7323 7324 7325 7326 7327 7328 7329 7330 8520 8521 8522 8523 8524 8525 8526 8527 8528 8529 8530 8531 8532 9960 9961 9962 9963 9964 9965 9966 9967 9968 9969 10920 10921 10922 10923 11340 11341 11342 11343 11344 11345 11346 11347 11348 11349 12120 12121 12122 12123 12124 12125 12126 12127 12128 12129 12130 12131 12960 12961 12962 12963 12964 12965 12966 12967 12968 12969 12970 12971 12972 12973 13020 13021 13022 13023 13024 13025 15540 16380 16381 16382 16383 16384 16385 16386 16387 16388 16389 16390 16391 16800 16801 16802 16803 16804 16805 20700 20701 20702 24180 24181 24182 24183 24184 24185 24360 24361 24362 24363 24364 24365 24366 24367 24368 24369 24370 24371 24840 24841 24842 24843 28260 28261 28262 28263 31080 31081 31082 31083 31084 31085 31086 33180 33181 33182 33183 33184 33185 33186 33187 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1026193 1026194 1026195 1026196 1026197 1026198 1026199 1041660 1041661 1041662 1041663 1041664 1041665 1041666 1041667 1041668 1041669 1041670 1041671 1041672 1108500 1110360 1110780 1154100 1154101 1154102 1154103 1154104 1154105 1154106 1154107 1154108 1154109 1154110 1154111 1154112 1154113 1167420 1167421 1167422 1167423 1167424 1167425 1167426 1167427 1167428 1167429 1167430 1197240 1197241 1197242 1242180 1242181 1242182 1242183 1242184 1242185 1242186 1242187 1242188 1242189 1242190 1242191 1242192 1242193 1242194 1242195 1242196 1242197 1242198 1242199 1286580 1286581 1286582 1286583 1286584 1286585 1462560 1462561 1462562 1462563 1462564 1462565 1462566 1462567 1462568 1462569 1462570 1645020 1645021 1645022 1645023 1645024 1645025 1645026 1645027 1645028 1645029 1659060 1659061 1659062 1659063 1676400 1676401 1676402 1676403 1676404 1676405 1676406 1676407 1676408 1676409 1676410 1676411 1694700 1694701 1694702 1694703 1694704 1694705 1694706 1694707 1694708 1694709 1694710 1694711 1703340 1703341 1703342 1703343 1703344 1703345 1794120 1794121 1794122 1794123 1794124 1794125 1794126 1794127 1794128 1794129 1794130 1794131 1794132 1794133 1794134 1900800 1900801 1900802 1900803 1900804 1900805 1900806 1900807 1900808 1900809 1900810 1900811 1900812 1900813 1900814 1900815 1969380 1969381 1969382 1969383 1984560 1984561 1984562 1984563 1984564 1984565 1984566 1984567 1984568 1984569 1999380 1999381 1999382 1999383 1999384 1999385 1999386 1999387 1999388 1999389 1999390 1999391 1999392 1999393 1999394 1999395 2002500 2002501 2002502 2002503 2002504 2002505 2002506 2002507 2002508 2002509 2002510 2002511 2002512 2002513 2002514 2002515 2007480 2007481 2007482 2007483 2007484 2007485 2007486 2007487 2007488 2007489 2007490 2007491 2007492 2007493 2007494 2136180 2136181 2136182 2136183 2136184 2136185 2136186 2136187 2136188 2136189 2136190 2136191 2136192 2136193 2136194 2136195 2136196 2136197 2215380 2215381 2215382 2215383 2215384 2215385 2356980 2356981 2356982 2356983 2359020 2359021 2359022 2359023 2359024 2359025 2359026 2359027 2359028 2359029 2359030 2359031 2359032 2359033 2359034 2359035 2359036 2359037 2409840 2430660] INFO 2025-06-26 11:42:58,595 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:42:58,601 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 11:42:58,602 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.227.08 ERROR 2025-06-26 11:42:58,602 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.227.08 INFO 2025-06-26 11:42:58,760 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_cal.nc INFO 2025-06-26 11:43:11,566 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, 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 11:43:11,571 process.py align():251 [1] Alignment steps for 2006.227.08 INFO 2025-06-26 11:43:11,608 align.py process_cal():139 [1] Processing dorado_2006.227.08_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.227.08 INFO 2025-06-26 11:43:11,661 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:43:11,667 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:43:11,794 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:43:11,802 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:43:11,928 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:43:11,936 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:43:12,017 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:43:12,017 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:43:12,071 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:43:12,080 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:43:12,204 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:43:12,211 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:12,321 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:43:12,328 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:12,440 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:43:12,447 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:12,556 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:12,563 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:12,675 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:12,682 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:12,793 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:12,799 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:12,910 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:12,917 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,027 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,034 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,144 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,151 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,260 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,267 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,377 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,387 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,509 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,621 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,627 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,736 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,743 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,856 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,862 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:13,972 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:13,980 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:14,092 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:14,099 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:14,210 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:14,217 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:14,326 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:14,333 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:14,445 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.227.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:43:14,452 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:43:14,592 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:43:14,687 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:43:14,782 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 11:43:14,877 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:43:14,980 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 11:43:15,067 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_align.nc INFO 2025-06-26 11:43:15,187 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, 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 11:43:15,190 process.py resample():273 [1] Resampling steps for 2006.227.08 INFO 2025-06-26 11:43:15,190 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:43:15,220 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_align.nc mission netCDF file INFO 2025-06-26 11:43:15,227 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_align.nc mission netCDF file INFO 2025-06-26 11:43:15,229 resample.py get_mission_start_end():1145 [1] navigation: 2006-08-15T03:08:08.444385280 to 2006-08-15T14:36:41.524245504 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:43:15,231 resample.py get_mission_start_end():1145 [1] hs2 : 2006-08-15T03:07:51.945515520 to 2006-08-15T14:36:41.344257792 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 11:43:15,233 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-08-15T03:08:15.143926272 to 2006-08-15T14:36:41.454250240 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 11:43:15,235 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-08-15T03:08:15.153925632 to 2006-08-15T14:36:41.494247424 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 11:43:15,237 resample.py get_mission_start_end():1145 [1] isus : 2006-08-15T03:09:09.570197760 to 2006-08-15T14:36:41.404253696 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 11:43:15,238 resample.py get_mission_start_end():1145 [1] biolume : 2006-08-15T03:07:46.425859328 to 2006-08-15T14:36:40.844257792 (0 days 00:00:00.679987712 before mission_end) INFO 2025-06-26 11:43:15,240 resample.py get_mission_start_end():1145 [1] tailcone : 2006-08-15T03:07:47.105847040 to 2006-08-15T14:36:41.424252160 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 11:43:15,241 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_align.nc mission netCDF file INFO 2025-06-26 11:43:15,242 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:15,672 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:15,742 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:15,810 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:15,879 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:15,939 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:15,998 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,057 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,114 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,168 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,227 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,281 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,335 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,389 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,444 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,498 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,552 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,611 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,667 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,723 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,779 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,834 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,890 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,913 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,934 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,953 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:16,976 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:17,041 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:43:17,374 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_1S.nc INFO 2025-06-26 11:43:19,005 create_products.py gulper_odv():401 [1] No gulper times found for 2006.227.08 INFO 2025-06-26 11:43:19,006 process.py archive():337 [1] Archiving steps for 2006.227.08 INFO 2025-06-26 11:43:19,006 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08, BASE_PATH = /data/auv_data INFO 2025-06-26 11:43:19,007 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:43:19,009 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.227.08_1S.nc INFO 2025-06-26 11:43:19,041 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:43:19,042 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.227.08_cal.nc INFO 2025-06-26 11:43:19,209 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:43:19,210 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.227.08_align.nc INFO 2025-06-26 11:43:19,359 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:43:19,401 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,440 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,444 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,473 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,598 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,606 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,663 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,700 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,828 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006227/2006.227.08 done. INFO 2025-06-26 11:43:19,828 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:43:19,828 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.227.08/dorado_2006.227.08_processing.log /Volumes/AUVCTD/surveys/2006/netcdf