INFO 2025-06-26 16:31:19,931 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 16:31:19,931 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey sixth - M0 to LatMix, aborted at 0500 local - 8 laps rqn out of battery - ctdToUse = ctd1 INFO 2025-06-26 16:31:19,931 process.py process_mission():449 [1] Processing AUVCTD mission 2010.285.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:31:19,931 process.py download_process():165 [1] Download and processing steps for 2010.285.00 INFO 2025-06-26 16:31:19,931 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010285/2010.285.00 INFO 2025-06-26 16:31:19,931 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010285/2010.285.00 to /data/auv_data/dorado/missionlogs/2010.285.00 INFO 2025-06-26 16:31:26,570 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.285.00 INFO 2025-06-26 16:31:26,570 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/ctdDriver.log (20394635 bytes) INFO 2025-06-26 16:31:28,053 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.285.00/ctdDriver.log: [ 61351 89642 91458 94322 109720 112241 113586 114797 123607 124254 130745 131737 132323 132387 135583 139438 139939 146554 146748 151935 154249 159250 160785 161746 164650 176922 179801 181232 182281 186976 189239 191737 199547 199823 206728 211957] INFO 2025-06-26 16:31:28,118 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/ctdDriver2.log (20394719 bytes) INFO 2025-06-26 16:31:29,612 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.285.00/ctdDriver2.log: [ 89644 91460 92096 94324 109722 112243 113588 114799 115694 123609 124256 129875 130747 131739 132325 132389 135585 137020 139440 139941 146556 151937 154251 159252 159392 160787 161748 164652 176924 179803 181811 182282 186977 189240 191738 199548 199824 206729 211958] INFO 2025-06-26 16:31:29,685 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/gps.log (342860 bytes) INFO 2025-06-26 16:31:29,732 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/hydroscatlog.log (17846662 bytes) INFO 2025-06-26 16:31:31,567 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.285.00/hydroscatlog.log: [ 37207 85461 93524 94398 95754 101832 107862 110057 111601 111938 113651 115939 116819 119515 120039 124313 126512 130801 137587 139989 145866 150052 151919 152578 156838 159291 160825 162037 164687 168735 169275 169874 176953 181178 182391 184264 186667 187003 191761 199567 209943] INFO 2025-06-26 16:31:31,629 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/navigation.log (62627918 bytes) INFO 2025-06-26 16:31:36,382 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/isuslog.log (1320149 bytes) INFO 2025-06-26 16:31:36,511 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.285.00/isuslog.log: [1 3] INFO 2025-06-26 16:31:36,516 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/parosci.log (23323958 bytes) INFO 2025-06-26 16:31:38,552 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/tailCone.log (12744523 bytes) INFO 2025-06-26 16:31:40,189 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/biolume.log (14843114 bytes) INFO 2025-06-26 16:31:41,725 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:31:42,470 logs2netcdfs.py download_process_logs():807 [1] Time to process: 15.90 seconds INFO 2025-06-26 16:31:42,470 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.285.00/lopc.bin (142590000 bytes) INFO 2025-06-26 16:31:42,470 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:31:42 2025 INFO 2025-06-26 16:31:42,470 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.285.00/parosci.nc INFO 2025-06-26 16:31:42,470 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:31:42,470 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.285.00/parosci.nc INFO 2025-06-26 16:31:42,474 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1286920085.2, sensor_off_time = 1286973230.1 INFO 2025-06-26 16:31:42,474 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 53144 seconds. Expecting to read 106288 L frames from the lopc.bin file. INFO 2025-06-26 16:31:42,474 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 106288 records from the lopc.bin file. INFO 2025-06-26 16:31:43,132 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-12 21:48:05 Z and endTime = 2010-10-13 12:33:50 Z with 106288 records expected to be read from lopc.bin INFO 2025-06-26 16:31:43,132 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.285.00/lopc.bin INFO 2025-06-26 16:31:43,132 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.285.00/lopc.nc INFO 2025-06-26 16:31:43,133 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.285.00/lopc.nc INFO 2025-06-26 16:31:43,133 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.285.00 INFO 2025-06-26 16:31:43,133 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 16:31:43,224 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:31:43,224 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:31:43,224 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:31:43,876 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 16:31:43,878 process.py calibrate():227 [1] Calibration steps for 2010.285.00 INFO 2025-06-26 16:31:44,274 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 16:31:44,276 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:31:45,091 calibrate.py _nudge_pos():1806 [1] 120: 0.200 0.0003316 -0.0004107 769 2.56 19.209 -29.725 2010-10-12T21:52:34.973341440 INFO 2025-06-26 16:31:45,751 calibrate.py _nudge_pos():1806 [1] 185: 0.010 -0.0038613 -0.0008065 11890 39.63 -14.445 -3.771 2010-10-12T22:33:17.176039168 INFO 2025-06-26 16:31:46,465 calibrate.py _nudge_pos():1806 [1] 256: 0.200 -0.0025108 -0.0003893 9789 32.63 -11.405 -2.211 2010-10-12T23:07:04.977125120 INFO 2025-06-26 16:31:47,125 calibrate.py _nudge_pos():1806 [1] 322: 0.010 -0.0031447 -0.0003658 15154 50.51 -9.222 -1.342 2010-10-12T23:58:41.175021056 INFO 2025-06-26 16:31:47,765 calibrate.py _nudge_pos():1806 [1] 383: 0.020 -0.0005042 -0.0008092 1590 5.30 -14.102 -28.310 2010-10-13T00:04:59.169126656 INFO 2025-06-26 16:31:48,583 calibrate.py _nudge_pos():1806 [1] 463: 0.020 0.0050604 0.0008252 28702 95.68 7.842 1.598 2010-10-13T01:41:59.170429440 INFO 2025-06-26 16:31:49,326 calibrate.py _nudge_pos():1806 [1] 534: 0.030 0.0033172 0.0000832 7389 24.63 19.975 0.626 2010-10-13T02:07:47.174383872 INFO 2025-06-26 16:31:50,078 calibrate.py _nudge_pos():1806 [1] 607: 0.040 -0.0005866 -0.0011711 2250 7.50 -11.606 -28.947 2010-10-13T02:16:29.168624896 INFO 2025-06-26 16:31:50,810 calibrate.py _nudge_pos():1806 [1] 678: 0.040 -0.0095129 -0.0017380 28742 95.83 -14.709 -3.361 2010-10-13T03:53:29.169927424 INFO 2025-06-26 16:31:51,427 calibrate.py _nudge_pos():1806 [1] 736: 0.030 0.0005148 -0.0001806 8711 29.05 2.625 -1.152 2010-10-13T04:23:29.176618496 INFO 2025-06-26 16:31:52,049 calibrate.py _nudge_pos():1806 [1] 795: 0.050 0.0001921 -0.0001010 999 3.33 8.545 -5.620 2010-10-13T04:27:47.168944896 INFO 2025-06-26 16:31:52,833 calibrate.py _nudge_pos():1806 [1] 870: 0.050 0.0055254 0.0007711 28649 95.56 8.573 1.495 2010-10-13T06:04:35.171069440 INFO 2025-06-26 16:31:53,642 calibrate.py _nudge_pos():1806 [1] 947: 0.050 0.0035087 -0.0000808 9844 32.83 15.851 -0.456 2010-10-13T06:38:41.170908928 INFO 2025-06-26 16:31:54,444 calibrate.py _nudge_pos():1806 [1] 1023: 0.060 -0.0001121 -0.0021406 3735 12.45 -1.336 -31.868 2010-10-13T06:52:23.174597632 INFO 2025-06-26 16:31:55,246 calibrate.py _nudge_pos():1806 [1] 1099: 0.060 -0.0096385 -0.0016673 29479 98.35 -14.523 -3.141 2010-10-13T08:31:59.175213568 INFO 2025-06-26 16:31:55,988 calibrate.py _nudge_pos():1806 [1] 1168: 0.070 -0.0001601 -0.0000978 9523 31.76 -0.747 -0.570 2010-10-13T09:04:53.169985792 INFO 2025-06-26 16:31:56,707 calibrate.py _nudge_pos():1806 [1] 1235: 0.080 -0.0001653 -0.0003570 720 2.40 -10.214 -27.600 2010-10-13T09:08:23.175599360 INFO 2025-06-26 16:31:57,443 calibrate.py _nudge_pos():1806 [1] 1304: 0.080 0.0046398 0.0008088 28350 94.56 7.275 1.585 2010-10-13T10:44:05.172245760 INFO 2025-06-26 16:31:58,227 calibrate.py _nudge_pos():1806 [1] 1375: 0.080 0.0032770 0.0002054 9183 30.63 15.867 1.242 2010-10-13T11:15:53.171538944 INFO 2025-06-26 16:31:59,005 calibrate.py _nudge_pos():1806 [1] 1447: 0.090 -0.0002031 -0.0012282 1925 6.41 -4.698 -35.487 2010-10-13T11:23:29.170300672 INFO 2025-06-26 16:31:59,805 calibrate.py _nudge_pos():1806 [1] 1519: 0.090 -0.0016349 -0.0003574 4590 15.31 -15.832 -4.325 2010-10-13T11:39:59.172480768 INFO 2025-06-26 16:32:35,180 calibrate.py _nudge_pos():1862 [1] 4699: - - - 5 0.01 - - INFO 2025-06-26 16:32:35,181 calibrate.py _nudge_pos():1868 [1] Points in final series = 265233 WARNING 2025-06-26 16:32:35,552 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:33:02,242 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 41 of 212407 INFO 2025-06-26 16:33:03,924 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:33:19,458 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:33:21,122 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:33:21,126 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.285.00/ctd1.nc INFO 2025-06-26 16:33:21,127 calibrate.py _range_qc_combined_nc():898 [1] Setting 7 ctd1_salinity values to NaN INFO 2025-06-26 16:33:21,128 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 16:33:21,128 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:33:33,189 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:33:34,775 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:33:34,778 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.285.00/ctd2.nc WARNING 2025-06-26 16:33:34,780 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (25206) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 16:33:34,780 calibrate.py _range_qc_combined_nc():898 [1] Setting 25206 ctd2_salinity values to NaN INFO 2025-06-26 16:33:34,781 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 16:33:34,781 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:33:36,776 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:33:39,165 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 72 73 74 75 76 77 78 79 80 120 121 337740 337741 337742 337743 337744 397860 454800 454801 508320 629940 629941 629942 629943 629944 629945 629946 667500 693180 789840 789841 805380 805381 805382 805383 805384 805385 864540 864541 864542 864543 864544 864545 864546 865440 865441 865442 865443 865444 865445 865446 865447 865448 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3056654 3056655 3056656 3056657 3105180 3105181 3105182 3105183 3105184 3105185 3105186 3105187 3105188 3105189 3105190 3105191 3105192 3105193 3105194] INFO 2025-06-26 16:33:39,621 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 16:34:28,682 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.285.00 ERROR 2025-06-26 16:34:28,682 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.285.00 INFO 2025-06-26 16:34:28,885 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_cal.nc INFO 2025-06-26 16:34:52,290 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 16:34:52,298 process.py align():251 [1] Alignment steps for 2010.285.00 INFO 2025-06-26 16:34:52,387 align.py process_cal():139 [1] Processing dorado_2010.285.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.285.00 INFO 2025-06-26 16:34:52,458 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:34:52,466 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 16:34:52,633 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:34:52,642 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 16:34:52,809 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:34:52,820 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 16:34:52,920 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:34:52,920 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:34:52,984 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:34:52,994 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 16:34:53,158 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:53,167 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:53,309 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:53,318 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:53,460 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:53,469 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:53,619 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:53,627 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:53,785 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:53,794 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:53,938 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:53,946 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:54,093 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:54,102 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:54,245 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:54,254 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:54,401 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:54,410 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:54,553 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:54,563 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:54,707 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:54,715 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:54,857 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:54,865 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,009 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,018 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,162 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,169 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,311 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,320 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,464 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,473 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,620 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,628 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,773 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,785 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:55,933 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:55,943 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:56,088 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:56,097 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:56,251 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:56,260 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:56,403 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.285.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:34:56,411 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:34:56,593 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:34:56,704 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:34:56,816 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:34:56,935 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:34:57,059 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:34:57,300 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.98 INFO 2025-06-26 16:34:58,670 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 16:34:58,783 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_align.nc INFO 2025-06-26 16:34:59,090 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 16:34:59,094 process.py resample():273 [1] Resampling steps for 2010.285.00 INFO 2025-06-26 16:34:59,095 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:34:59,175 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_align.nc mission netCDF file INFO 2025-06-26 16:34:59,183 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_align.nc mission netCDF file INFO 2025-06-26 16:34:59,185 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-12T21:48:53.788493568 to 2010-10-13T12:33:50.171142400 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:34:59,188 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-12T21:48:11.501390336 to 2010-10-13T12:33:50.101147136 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 16:34:59,190 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-12T21:48:41.759317760 to 2010-10-13T12:33:50.121145600 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 16:34:59,192 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-12T21:48:41.569330688 to 2010-10-13T12:33:50.121145600 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 16:34:59,194 resample.py get_mission_start_end():1145 [1] isus : 2010-10-12T21:49:03.617820160 to 2010-10-13T12:33:49.561184256 (0 days 00:00:00.609958144 before mission_end) INFO 2025-06-26 16:34:59,196 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-12T21:48:03.891877632 to 2010-10-13T12:33:49.091182080 (0 days 00:00:01.079960320 before mission_end) INFO 2025-06-26 16:34:59,198 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-12T21:48:05.511800832 to 2010-10-13T12:33:50.131144960 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 16:34:59,199 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_align.nc mission netCDF file INFO 2025-06-26 16:34:59,200 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:34:59,753 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:34:59,842 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:34:59,927 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,018 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,093 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,167 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,240 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,311 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,379 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,446 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,514 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,582 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,648 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,715 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,782 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,849 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,916 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:00,986 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,058 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,179 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,249 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,319 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,389 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,459 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,488 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,515 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,540 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,567 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,592 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:01,601 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:35:01,601 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:35:03,628 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:35:04,127 resample.py add_biolume_proxies():633 [1] Zero flow values found: 19045 of 53147 - replaced with 350 ml/s INFO 2025-06-26 16:35:04,128 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:35:04,351 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:35:04,438 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:35:04,502 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:35:04,502 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:35:04,595 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:35:05,013 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_1S.nc INFO 2025-06-26 16:35:07,992 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 16:35:17,994 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.285.00/dorado_2010.285.00_1S_Gulper.txt INFO 2025-06-26 16:35:17,995 process.py archive():337 [1] Archiving steps for 2010.285.00 INFO 2025-06-26 16:35:17,995 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00, BASE_PATH = /data/auv_data INFO 2025-06-26 16:35:17,996 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:35:17,997 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.285.00_1S.nc INFO 2025-06-26 16:35:18,041 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:35:18,042 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.285.00_cal.nc INFO 2025-06-26 16:35:18,375 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:35:18,376 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.285.00_align.nc INFO 2025-06-26 16:35:18,862 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:35:18,922 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:18,982 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:18,987 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,037 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,204 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,213 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,283 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,328 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,486 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,492 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010285/2010.285.00 done. INFO 2025-06-26 16:35:19,492 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:35:19,493 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.285.00_1S_Gulper.txt INFO 2025-06-26 16:35:19,497 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.285.00/dorado_2010.285.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 16:35:19,497 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.285.00/dorado_2010.285.00_processing.log /Volumes/AUVCTD/surveys/2010/netcdf