INFO 2025-06-26 13:55:38,231 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 13:55:38,231 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy group missions over canyon axis between M0 & M1 (gulper trips in nice layers) - ctdToUse = ctd1 INFO 2025-06-26 13:55:38,231 process.py process_mission():449 [1] Processing AUVCTD mission 2008.010.10 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:55:38,231 process.py download_process():165 [1] Download and processing steps for 2008.010.10 INFO 2025-06-26 13:55:38,232 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008010/2008.010.10 INFO 2025-06-26 13:55:38,232 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008010/2008.010.10 to /data/auv_data/dorado/missionlogs/2008.010.10 INFO 2025-06-26 13:55:39,972 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.010.10 INFO 2025-06-26 13:55:39,972 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/ctdDriver.log (1630758 bytes) INFO 2025-06-26 13:55:40,116 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/ctdDriver2.log (1630943 bytes) INFO 2025-06-26 13:55:40,251 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/gps.log (30020 bytes) INFO 2025-06-26 13:55:40,263 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/hydroscatlog.log (1022594 bytes) INFO 2025-06-26 13:55:40,394 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/navigation.log (4995302 bytes) INFO 2025-06-26 13:55:40,806 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/isuslog.log (105461 bytes) INFO 2025-06-26 13:55:40,821 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.010.10/isuslog.log: [1 2 3 4 5 6 7 9] INFO 2025-06-26 13:55:40,822 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/parosci.log (1674326 bytes) INFO 2025-06-26 13:55:40,985 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/tailCone.log (216523 bytes) INFO 2025-06-26 13:55:41,020 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/biolume.log (1162940 bytes) INFO 2025-06-26 13:55:41,135 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:55:41,205 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.23 seconds INFO 2025-06-26 13:55:41,206 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.010.10/lopc.bin (12646883 bytes) INFO 2025-06-26 13:55:41,206 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 13:55:41 2025 INFO 2025-06-26 13:55:41,206 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.010.10/parosci.nc INFO 2025-06-26 13:55:41,206 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 13:55:41,206 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.010.10/parosci.nc INFO 2025-06-26 13:55:41,209 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1200002417.5, sensor_off_time = 1200006673.9 INFO 2025-06-26 13:55:41,209 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 4256 seconds. Expecting to read 8512 L frames from the lopc.bin file. INFO 2025-06-26 13:55:41,209 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 8512 records from the lopc.bin file. INFO 2025-06-26 13:55:41,262 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-01-10 22:00:17 Z and endTime = 2008-01-10 23:11:13 Z with 8512 records expected to be read from lopc.bin INFO 2025-06-26 13:55:41,262 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.010.10/lopc.bin INFO 2025-06-26 13:55:41,262 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.010.10/lopc.nc INFO 2025-06-26 13:55:41,263 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.010.10/lopc.nc INFO 2025-06-26 13:55:41,263 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.010.10 INFO 2025-06-26 13:55:41,264 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 13:55:41,295 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 13:55:41,295 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 13:55:41,295 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 13:55:42,211 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 13:55:42,211 process.py calibrate():227 [1] Calibration steps for 2008.010.10 INFO 2025-06-26 13:55:42,316 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 13:55:42,318 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:55:42,744 calibrate.py _nudge_pos():1806 [1] 69: 0.100 0.0005564 -0.0001532 1965 6.55 12.612 -4.337 2008-01-10T22:07:53.720224768 INFO 2025-06-26 13:55:44,051 calibrate.py _nudge_pos():1806 [1] 211: 0.090 0.0041926 -0.0000004 7395 24.65 25.250 -0.003 2008-01-10T22:34:53.729246720 INFO 2025-06-26 13:55:44,117 calibrate.py _nudge_pos():1806 [1] 218: 0.090 0.0000366 -0.0000180 210 0.70 7.788 -4.785 2008-01-10T22:35:41.725958656 INFO 2025-06-26 13:55:44,980 calibrate.py _nudge_pos():1806 [1] 312: 0.100 -0.0001221 0.0010065 9735 32.45 -0.559 5.748 2008-01-10T23:09:41.726209280 INFO 2025-06-26 13:55:45,854 calibrate.py _nudge_pos():1862 [1] 376: - - - 1 0.00 - - INFO 2025-06-26 13:55:45,854 calibrate.py _nudge_pos():1868 [1] Points in final series = 21158 WARNING 2025-06-26 13:55:45,972 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 13:55:46,148 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:46,326 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 11 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:46,458 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 11 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:46,460 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.010.10/ctd1.nc INFO 2025-06-26 13:55:46,461 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:55:46,461 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 13:55:46,462 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:55:46,628 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 10 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:46,762 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 10 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:55:46,764 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.010.10/ctd2.nc INFO 2025-06-26 13:55:46,765 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 13:55:46,766 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 13:55:46,766 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:55:46,931 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:55:47,117 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 1620 1621 1622 12720 12721 12722 12723 16800 16801 16802 16980 24480 35040 35041 35042 76860 76861 93960 113940 113941 113942 113943 113944 113945 119520 232620 232621 232622] INFO 2025-06-26 13:55:47,159 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -8 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:55:47,165 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 13:55:47,165 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2008.010.10 ERROR 2025-06-26 13:55:47,166 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.010.10 INFO 2025-06-26 13:55:47,173 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_cal.nc INFO 2025-06-26 13:55:47,227 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_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_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 13:55:47,233 process.py align():251 [1] Alignment steps for 2008.010.10 INFO 2025-06-26 13:55:47,259 align.py process_cal():139 [1] Processing dorado_2008.010.10_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.010.10 INFO 2025-06-26 13:55:47,270 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:47,272 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:47,294 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:47,297 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:47,319 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:47,322 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:47,335 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:55:47,335 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:55:47,343 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:55:47,346 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 13:55:47,367 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,369 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,389 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,392 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,411 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,414 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,435 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,437 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,458 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,460 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,480 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,482 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,505 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,526 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,528 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,549 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,551 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,571 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,573 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,593 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,596 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,616 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,619 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,638 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,641 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,661 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,663 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,683 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,685 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,707 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,710 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,731 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,734 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,755 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,757 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,779 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,782 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,803 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,806 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,828 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,831 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,851 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.010.10_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:55:47,854 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:55:47,878 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:47,898 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:47,918 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:55:47,940 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:55:47,962 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.06 INFO 2025-06-26 13:55:47,974 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_align.nc INFO 2025-06-26 13:55:48,026 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_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_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 13:55:48,028 process.py resample():273 [1] Resampling steps for 2008.010.10 INFO 2025-06-26 13:55:48,029 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:55:48,053 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_align.nc mission netCDF file INFO 2025-06-26 13:55:48,058 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_align.nc mission netCDF file INFO 2025-06-26 13:55:48,059 resample.py get_mission_start_end():1145 [1] navigation: 2008-01-10T22:00:42.589759232 to 2008-01-10T23:11:13.919893504 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:55:48,061 resample.py get_mission_start_end():1145 [1] hs2 : 2008-01-10T22:00:15.051645696 to 2008-01-10T23:11:13.679909888 (0 days 00:00:00.239983616 before mission_end) INFO 2025-06-26 13:55:48,062 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-01-10T22:00:28.600717824 to 2008-01-10T23:11:13.759904512 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 13:55:48,063 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-01-10T22:00:28.380732672 to 2008-01-10T23:11:13.769903616 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 13:55:48,065 resample.py get_mission_start_end():1145 [1] isus : 2008-01-10T22:01:10.217866752 to 2008-01-10T23:11:12.799970048 (0 days 00:00:01.119923456 before mission_end) INFO 2025-06-26 13:55:48,066 resample.py get_mission_start_end():1145 [1] biolume : 2008-01-10T22:00:09.172014592 to 2008-01-10T23:11:12.649946112 (0 days 00:00:01.269947392 before mission_end) INFO 2025-06-26 13:55:48,068 resample.py get_mission_start_end():1145 [1] tailcone : 2008-01-10T22:00:14.691670528 to 2008-01-10T23:11:13.309935104 (0 days 00:00:00.609958400 before mission_end) INFO 2025-06-26 13:55:48,068 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_align.nc mission netCDF file INFO 2025-06-26 13:55:48,069 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,138 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,153 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,167 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,182 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,196 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,210 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,223 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,236 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,248 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,261 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,273 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,285 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,298 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,310 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,322 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,334 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,348 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,362 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,376 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,389 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,403 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,416 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,431 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,446 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,457 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,467 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,477 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,487 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,498 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:55:48,620 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_1S.nc INFO 2025-06-26 13:55:50,226 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:55:54,634 create_products.py gulper_odv():522 [1] Wrote 4 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.010.10/dorado_2008.010.10_1S_Gulper.txt INFO 2025-06-26 13:55:54,634 process.py archive():337 [1] Archiving steps for 2008.010.10 INFO 2025-06-26 13:55:54,634 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10, BASE_PATH = /data/auv_data INFO 2025-06-26 13:55:54,636 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 13:55:54,636 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.10_1S.nc INFO 2025-06-26 13:55:54,646 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:54,646 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.10_cal.nc INFO 2025-06-26 13:55:54,670 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:54,671 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.010.10_align.nc INFO 2025-06-26 13:55:54,694 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 13:55:54,706 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,717 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,722 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,730 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,749 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,754 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,763 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,769 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,784 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,795 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008010/2008.010.10 done. INFO 2025-06-26 13:55:54,795 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:55:54,797 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.010.10_1S_Gulper.txt INFO 2025-06-26 13:55:54,801 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.010.10/dorado_2008.010.10_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 13:55:54,801 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.010.10/dorado_2008.010.10_processing.log /Volumes/AUVCTD/surveys/2008/netcdf