INFO 2025-06-26 19:23:01,525 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 19:23:01,525 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2012 - Distributed Autonomy - ctdToUse = ctd1 INFO 2025-06-26 19:23:01,525 process.py process_mission():449 [1] Processing CANON September 2012 mission 2012.269.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:23:01,525 process.py download_process():165 [1] Download and processing steps for 2012.269.00 INFO 2025-06-26 19:23:01,525 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012269/2012.269.00 INFO 2025-06-26 19:23:01,526 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012269/2012.269.00 to /data/auv_data/dorado/missionlogs/2012.269.00 INFO 2025-06-26 19:23:05,138 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.269.00 INFO 2025-06-26 19:23:05,138 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/ctdDriver.log (7001478 bytes) INFO 2025-06-26 19:23:05,662 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/ctdDriver2.log (7004063 bytes) INFO 2025-06-26 19:23:06,176 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/gps.log (292388 bytes) INFO 2025-06-26 19:23:06,213 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/hydroscatlog.log (6136306 bytes) INFO 2025-06-26 19:23:06,892 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/navigation.log (24804630 bytes) INFO 2025-06-26 19:23:08,654 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/isuslog.log (541173 bytes) INFO 2025-06-26 19:23:08,708 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/parosci.log (7428710 bytes) INFO 2025-06-26 19:23:09,344 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/tailCone.log (4386187 bytes) INFO 2025-06-26 19:23:09,880 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/biolume.log (5105890 bytes) INFO 2025-06-26 19:23:10,378 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:23:10,643 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.50 seconds INFO 2025-06-26 19:23:10,643 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2012.269.00/lopc.bin (76524239 bytes) INFO 2025-06-26 19:23:10,643 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:23:10 2025 INFO 2025-06-26 19:23:10,643 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2012.269.00/parosci.nc INFO 2025-06-26 19:23:10,643 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:23:10,643 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2012.269.00/parosci.nc INFO 2025-06-26 19:23:10,647 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1348590933.0, sensor_off_time = 1348609206.9 INFO 2025-06-26 19:23:10,647 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 18273 seconds. Expecting to read 36546 L frames from the lopc.bin file. INFO 2025-06-26 19:23:10,647 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 36546 records from the lopc.bin file. INFO 2025-06-26 19:23:10,860 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2012-09-25 16:35:32 Z and endTime = 2012-09-25 21:40:06 Z with 36546 records expected to be read from lopc.bin INFO 2025-06-26 19:23:10,861 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2012.269.00/lopc.bin INFO 2025-06-26 19:23:10,861 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2012.269.00/lopc.nc INFO 2025-06-26 19:23:10,861 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2012.269.00/lopc.nc INFO 2025-06-26 19:23:10,861 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2012.269.00 INFO 2025-06-26 19:23:10,862 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:23:10,919 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:23:10,919 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:23:10,919 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:23:12,398 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:23:12,399 process.py calibrate():227 [1] Calibration steps for 2012.269.00 INFO 2025-06-26 19:23:12,570 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 19:23:12,572 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:23:17,193 calibrate.py _nudge_pos():1806 [1] 531: 0.150 -0.0022871 -0.0045462 9150 30.50 -11.119 -27.623 2012-09-25T17:14:52.008409088 INFO 2025-06-26 19:23:18,339 calibrate.py _nudge_pos():1806 [1] 655: 0.160 0.0028128 -0.0011536 8955 29.85 13.972 -7.162 2012-09-25T17:46:46.007291136 INFO 2025-06-26 19:23:19,593 calibrate.py _nudge_pos():1806 [1] 790: 0.160 0.0024114 -0.0011446 4370 14.56 24.551 -14.564 2012-09-25T18:03:34.008238336 INFO 2025-06-26 19:23:35,070 calibrate.py _nudge_pos():1806 [1] 2367: 0.160 0.0032772 -0.0069040 8950 29.83 16.291 -42.886 2012-09-25T18:59:40.007651584 INFO 2025-06-26 19:23:36,395 calibrate.py _nudge_pos():1806 [1] 2477: 0.170 -0.0016198 -0.0019381 8305 27.68 -8.677 -12.974 2012-09-25T19:29:10.006398208 INFO 2025-06-26 19:23:39,164 calibrate.py _nudge_pos():1806 [1] 2713: 0.170 0.0000347 -0.0022089 8935 29.78 0.173 -13.744 2012-09-25T20:02:52.007881728 INFO 2025-06-26 19:23:45,043 calibrate.py _nudge_pos():1806 [1] 3159: 0.180 -0.0023231 -0.0019637 8094 26.98 -12.771 -13.487 2012-09-25T20:37:16.006488064 INFO 2025-06-26 19:23:47,753 calibrate.py _nudge_pos():1806 [1] 3389: 0.180 -0.0013836 -0.0024804 8300 27.66 -7.419 -16.615 2012-09-25T21:08:45.007082752 INFO 2025-06-26 19:23:50,505 calibrate.py _nudge_pos():1806 [1] 3632: 0.190 0.0004921 -0.0001810 6115 20.38 3.581 -1.646 2012-09-25T21:33:10.006723328 INFO 2025-06-26 19:23:55,761 calibrate.py _nudge_pos():1862 [1] 4012: - - - 4 0.01 - - INFO 2025-06-26 19:23:55,761 calibrate.py _nudge_pos():1868 [1] Points in final series = 91040 WARNING 2025-06-26 19:23:55,950 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:23:56,166 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 6 of 73039 INFO 2025-06-26 19:23:56,750 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:23:57,684 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:23:58,275 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:23:58,277 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.269.00/ctd1.nc INFO 2025-06-26 19:23:58,278 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:23:58,279 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 19:23:58,279 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:23:59,114 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:23:59,912 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 36 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:23:59,915 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.269.00/ctd2.nc INFO 2025-06-26 19:23:59,917 calibrate.py _range_qc_combined_nc():898 [1] Setting 4 ctd2_salinity values to NaN INFO 2025-06-26 19:23:59,917 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 19:23:59,917 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:23:59,966 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:24:00,975 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65] INFO 2025-06-26 19:24:01,176 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:24:21,379 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2012.269.00 ERROR 2025-06-26 19:24:21,380 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.269.00 INFO 2025-06-26 19:24:21,478 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_cal.nc INFO 2025-06-26 19:24:21,639 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 19:24:21,645 process.py align():251 [1] Alignment steps for 2012.269.00 INFO 2025-06-26 19:24:21,685 align.py process_cal():139 [1] Processing dorado_2012.269.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.269.00 INFO 2025-06-26 19:24:21,715 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:24:21,719 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:24:21,805 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:24:21,812 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:24:21,903 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:24:21,909 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:24:21,958 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:24:21,958 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:24:21,995 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:24:22,002 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:24:22,097 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,104 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,183 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,189 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,268 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,275 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,354 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,361 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,455 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,460 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,519 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,524 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,584 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,590 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,678 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,685 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,769 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,776 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,841 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,847 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,906 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:22,911 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:22,995 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,003 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,098 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,104 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,170 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,175 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,252 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,259 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,341 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,349 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,432 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,439 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,508 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,513 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,573 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,578 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,636 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,641 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,702 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,707 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,767 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.269.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:24:23,772 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:24:23,843 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:24:23,900 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:24:23,981 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:24:24,061 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:24:24,126 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:24:24,210 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:24:24,706 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:24:24,783 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_align.nc INFO 2025-06-26 19:24:24,995 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 19:24:24,998 process.py resample():273 [1] Resampling steps for 2012.269.00 INFO 2025-06-26 19:24:25,000 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:24:25,055 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_align.nc mission netCDF file INFO 2025-06-26 19:24:25,066 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_align.nc mission netCDF file INFO 2025-06-26 19:24:25,069 resample.py get_mission_start_end():1145 [1] navigation: 2012-09-25T16:36:09.817489920 to 2012-09-25T21:40:06.808170496 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 19:24:25,072 resample.py get_mission_start_end():1145 [1] hs2 : 2012-09-25T16:35:39.109593600 to 2012-09-25T21:40:06.908163584 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:24:25,076 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-09-25T16:36:16.337043200 to 2012-09-25T21:40:06.848167680 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 19:24:25,079 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-09-25T16:36:09.067541248 to 2012-09-25T21:40:06.908163584 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:24:25,082 resample.py get_mission_start_end():1145 [1] isus : 2012-09-25T16:36:48.584834048 to 2012-09-25T21:40:06.278206720 (0 days 00:00:00.629956864 before mission_end) INFO 2025-06-26 19:24:25,084 resample.py get_mission_start_end():1145 [1] biolume : 2012-09-25T16:35:32.270027776 to 2012-09-25T21:40:05.988192256 (0 days 00:00:00.919971328 before mission_end) INFO 2025-06-26 19:24:25,087 resample.py get_mission_start_end():1145 [1] tailcone : 2012-09-25T16:35:33.539975168 to 2012-09-25T21:40:06.878165760 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 19:24:25,088 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_align.nc mission netCDF file INFO 2025-06-26 19:24:25,089 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,418 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,467 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,514 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,560 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,603 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,638 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,673 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,704 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,733 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,763 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,791 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,821 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,850 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,879 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,907 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,936 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,965 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:25,997 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,030 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,063 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,095 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,127 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,159 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,191 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,210 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,226 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,242 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,257 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,270 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:26,275 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:24:26,276 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:24:26,957 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:24:27,102 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:24:27,195 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:24:27,238 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:24:27,282 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:24:27,282 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:24:27,341 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:24:27,729 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_1S.nc INFO 2025-06-26 19:24:30,258 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:24:41,549 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2012.269.00/dorado_2012.269.00_1S_Gulper.txt INFO 2025-06-26 19:24:41,549 process.py archive():337 [1] Archiving steps for 2012.269.00 INFO 2025-06-26 19:24:41,549 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:24:41,551 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:24:41,552 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.269.00_1S.nc INFO 2025-06-26 19:24:41,574 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:24:41,575 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.269.00_cal.nc INFO 2025-06-26 19:24:41,702 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:24:41,704 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.269.00_align.nc INFO 2025-06-26 19:24:41,897 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:24:41,920 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:41,943 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:41,948 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:41,967 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,034 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,041 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,064 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,083 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,132 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,139 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012269/2012.269.00 done. INFO 2025-06-26 19:24:42,139 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:24:42,141 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2012/odv/dorado_2012.269.00_1S_Gulper.txt INFO 2025-06-26 19:24:42,145 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2012.269.00/dorado_2012.269.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2012/odv done. INFO 2025-06-26 19:24:42,145 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.269.00/dorado_2012.269.00_processing.log /Volumes/AUVCTD/surveys/2012/netcdf