INFO 2025-06-26 20:31:37,821 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 20:31:37,821 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB September 2014 with rhodamine sensor on ctdDriver2, channel 1 - ctdToUse = ctd1 INFO 2025-06-26 20:31:37,821 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.267.07 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:31:37,821 process.py download_process():165 [1] Download and processing steps for 2014.267.07 INFO 2025-06-26 20:31:37,822 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014267/2014.267.07 INFO 2025-06-26 20:31:37,822 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014267/2014.267.07 to /data/auv_data/dorado/missionlogs/2014.267.07 INFO 2025-06-26 20:31:43,249 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.267.07 INFO 2025-06-26 20:31:43,249 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/ctdDriver.log (10070598 bytes) INFO 2025-06-26 20:31:44,376 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/ctdDriver2.log (10070595 bytes) INFO 2025-06-26 20:31:45,547 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/gps.log (860396 bytes) INFO 2025-06-26 20:31:45,732 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/hydroscatlog.log (8830942 bytes) INFO 2025-06-26 20:31:46,831 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/navigation.log (37794402 bytes) INFO 2025-06-26 20:31:50,239 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/isuslog.log (653525 bytes) INFO 2025-06-26 20:31:50,313 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.267.07/isuslog.log: [2 3 4 5 6 7 8 9] INFO 2025-06-26 20:31:50,316 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/parosci.log (12398198 bytes) INFO 2025-06-26 20:31:51,385 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/tailCone.log (6310411 bytes) INFO 2025-06-26 20:31:52,236 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/biolume.log (7345230 bytes) INFO 2025-06-26 20:31:53,331 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:31:53,716 logs2netcdfs.py download_process_logs():807 [1] Time to process: 10.47 seconds INFO 2025-06-26 20:31:53,716 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.267.07/lopc.bin (26765816 bytes) INFO 2025-06-26 20:31:53,716 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:31:53 2025 INFO 2025-06-26 20:31:53,716 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.267.07/parosci.nc INFO 2025-06-26 20:31:53,716 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:31:53,716 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.267.07/parosci.nc INFO 2025-06-26 20:31:53,720 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1411573378.2, sensor_off_time = 1411599669.3 INFO 2025-06-26 20:31:53,720 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 26291 seconds. Expecting to read 52582 L frames from the lopc.bin file. INFO 2025-06-26 20:31:53,720 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 52582 records from the lopc.bin file. INFO 2025-06-26 20:31:54,220 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-09-24 15:42:58 Z and endTime = 2014-09-24 23:01:09 Z with 52582 records expected to be read from lopc.bin INFO 2025-06-26 20:31:54,220 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.267.07/lopc.bin INFO 2025-06-26 20:31:54,220 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.267.07/lopc.nc INFO 2025-06-26 20:31:54,221 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.267.07/lopc.nc INFO 2025-06-26 20:31:54,222 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.267.07 INFO 2025-06-26 20:31:54,222 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 20:31:54,226 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:31:54,228 process.py calibrate():227 [1] Calibration steps for 2014.267.07 INFO 2025-06-26 20:31:54,670 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 20:31:54,671 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:31:55,586 calibrate.py _nudge_pos():1806 [1] 127: 0.040 -0.0005990 -0.0001713 785 2.61 -34.034 -12.147 2014-09-24T15:47:39.212581120 INFO 2025-06-26 20:31:57,749 calibrate.py _nudge_pos():1806 [1] 318: 0.040 -0.0098637 -0.0015665 15430 51.43 -28.466 -5.644 2014-09-24T16:42:15.218159104 INFO 2025-06-26 20:32:55,597 calibrate.py _nudge_pos():1806 [1] 5520: 0.050 -0.0027512 -0.0000749 5195 17.31 -23.589 -0.802 2014-09-24T18:26:15.210690560 INFO 2025-06-26 20:32:56,626 calibrate.py _nudge_pos():1806 [1] 5600: 0.060 -0.0051041 0.0001492 10165 33.88 -22.371 0.816 2014-09-24T19:01:27.216008192 INFO 2025-06-26 20:33:09,299 calibrate.py _nudge_pos():1806 [1] 6709: 0.070 -0.0083828 -0.0000466 14050 46.83 -26.569 -0.185 2014-09-24T20:06:45.217606656 INFO 2025-06-26 20:33:10,281 calibrate.py _nudge_pos():1806 [1] 6787: 0.080 -0.0092298 0.0023070 12750 42.50 -32.225 10.059 2014-09-24T20:50:32.217645056 INFO 2025-06-26 20:33:11,218 calibrate.py _nudge_pos():1806 [1] 6863: 0.080 -0.0012410 0.0002109 2630 8.76 -21.012 4.460 2014-09-24T21:00:33.216473600 INFO 2025-06-26 20:34:01,900 calibrate.py _nudge_pos():1806 [1] 11541: 0.090 -0.0007767 0.0004797 2895 9.65 -11.955 9.215 2014-09-24T22:28:09.216412928 INFO 2025-06-26 20:34:02,695 calibrate.py _nudge_pos():1806 [1] 11621: 0.090 -0.0007872 -0.0000173 2500 8.33 -14.033 -0.385 2014-09-24T22:37:48.216748800 INFO 2025-06-26 20:34:03,781 calibrate.py _nudge_pos():1806 [1] 11728: 0.090 -0.0021065 0.0001907 5425 18.08 -17.298 1.955 2014-09-24T22:57:39.215159808 INFO 2025-06-26 20:34:05,882 calibrate.py _nudge_pos():1862 [1] 11890: - - - 5 0.01 - - INFO 2025-06-26 20:34:05,883 calibrate.py _nudge_pos():1868 [1] Points in final series = 131222 INFO 2025-06-26 20:34:06,261 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 12 of 105118 INFO 2025-06-26 20:34:07,080 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:34:08,071 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 67 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:34:08,844 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 67 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:34:08,847 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.267.07/ctd1.nc INFO 2025-06-26 20:34:08,848 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 20:34:08,849 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 20:34:08,849 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:34:09,783 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 67 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:34:10,565 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 67 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:34:10,568 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.267.07/ctd2.nc INFO 2025-06-26 20:34:10,569 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:34:10,570 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 20:34:10,570 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:34:11,543 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:34:13,213 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] INFO 2025-06-26 20:34:13,454 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:34:42,641 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.267.07 ERROR 2025-06-26 20:34:42,642 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.267.07 INFO 2025-06-26 20:34:42,753 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_cal.nc INFO 2025-06-26 20:34:42,948 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 20:34:42,954 process.py align():251 [1] Alignment steps for 2014.267.07 INFO 2025-06-26 20:34:43,005 align.py process_cal():139 [1] Processing dorado_2014.267.07_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.267.07 INFO 2025-06-26 20:34:43,049 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:34:43,054 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:34:43,158 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:34:43,165 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:34:43,269 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:34:43,276 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:34:43,332 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:34:43,332 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:34:43,370 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:34:43,376 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:34:43,469 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:43,475 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:43,561 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:43,567 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:43,689 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:43,698 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:43,823 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:43,831 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:43,922 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:43,929 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,017 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,023 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,107 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,113 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,202 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,209 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,293 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,299 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,381 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,388 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,475 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,481 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,561 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,567 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,663 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,672 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,793 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,802 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:44,899 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:44,906 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,016 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,026 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,137 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,143 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,219 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,225 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,301 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,307 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,382 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,388 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,467 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,473 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,552 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.267.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:34:45,558 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:34:45,658 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:34:45,725 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:34:45,794 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:34:45,865 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:34:45,945 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:34:46,087 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:34:46,770 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:34:46,830 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_align.nc INFO 2025-06-26 20:34:47,009 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 20:34:47,012 process.py resample():273 [1] Resampling steps for 2014.267.07 INFO 2025-06-26 20:34:47,013 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:34:47,055 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_align.nc mission netCDF file INFO 2025-06-26 20:34:47,061 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_align.nc mission netCDF file INFO 2025-06-26 20:34:47,063 resample.py get_mission_start_end():1145 [1] navigation: 2014-09-24T15:43:45.028623872 to 2014-09-24T23:01:09.210774272 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:34:47,065 resample.py get_mission_start_end():1145 [1] hs2 : 2014-09-24T15:43:02.351547136 to 2014-09-24T23:01:09.160777472 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 20:34:47,067 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-09-24T15:44:06.157176320 to 2014-09-24T23:01:09.060784384 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:34:47,069 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-09-24T15:44:06.117179136 to 2014-09-24T23:01:09.040785664 (0 days 00:00:00.169988608 before mission_end) INFO 2025-06-26 20:34:47,070 resample.py get_mission_start_end():1145 [1] isus : 2014-09-24T15:44:09.246964736 to 2014-09-24T23:01:08.710808320 (0 days 00:00:00.499965952 before mission_end) INFO 2025-06-26 20:34:47,072 resample.py get_mission_start_end():1145 [1] biolume : 2014-09-24T15:42:56.351924224 to 2014-09-24T23:01:07.800836608 (0 days 00:00:01.409937664 before mission_end) INFO 2025-06-26 20:34:47,074 resample.py get_mission_start_end():1145 [1] tailcone : 2014-09-24T15:42:57.941849344 to 2014-09-24T23:01:09.200774912 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 20:34:47,074 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_align.nc mission netCDF file INFO 2025-06-26 20:34:47,075 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,353 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,400 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,447 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,494 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,534 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,574 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,614 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,654 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,691 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,728 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,764 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,800 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,836 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,873 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,910 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,946 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:47,983 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,023 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,061 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,100 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,139 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,178 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,217 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,254 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,272 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,289 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,304 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,319 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,334 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:48,339 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:34:48,339 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:34:49,266 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:34:49,438 resample.py add_biolume_proxies():633 [1] Zero flow values found: 24721 of 26292 - replaced with 350 ml/s INFO 2025-06-26 20:34:49,438 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:34:49,528 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:34:49,568 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:34:49,601 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:34:49,601 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:34:49,653 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:34:49,925 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_1S.nc INFO 2025-06-26 20:34:52,600 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:35:10,924 create_products.py gulper_odv():522 [1] Wrote 16 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.267.07/dorado_2014.267.07_1S_Gulper.txt INFO 2025-06-26 20:35:10,924 process.py archive():337 [1] Archiving steps for 2014.267.07 INFO 2025-06-26 20:35:10,924 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07, BASE_PATH = /data/auv_data INFO 2025-06-26 20:35:10,927 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:35:10,929 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.267.07_1S.nc INFO 2025-06-26 20:35:10,960 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:35:10,961 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.267.07_cal.nc INFO 2025-06-26 20:35:11,135 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:35:11,136 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.267.07_align.nc INFO 2025-06-26 20:35:11,383 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:35:11,415 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,445 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,453 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,481 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,586 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,593 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,630 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,654 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,735 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,739 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014267/2014.267.07 done. INFO 2025-06-26 20:35:11,740 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:35:11,741 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.267.07_1S_Gulper.txt INFO 2025-06-26 20:35:11,745 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.267.07/dorado_2014.267.07_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:35:11,746 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.267.07/dorado_2014.267.07_processing.log /Volumes/AUVCTD/surveys/2014/netcdf