INFO 2025-06-26 14:44:01,898 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 14:44:01,898 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - On N-S line by M0 for ESP deployment - ctdToUse = ctd2 INFO 2025-06-26 14:44:01,898 process.py process_mission():449 [1] Processing AUVCTD mission 2009.113.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:44:01,898 process.py download_process():165 [1] Download and processing steps for 2009.113.00 INFO 2025-06-26 14:44:01,898 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009113/2009.113.00 INFO 2025-06-26 14:44:01,898 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009113/2009.113.00 to /data/auv_data/dorado/missionlogs/2009.113.00 INFO 2025-06-26 14:44:05,086 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.113.00 INFO 2025-06-26 14:44:05,086 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/ctdDriver.log (3102220 bytes) INFO 2025-06-26 14:44:05,318 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/ctdDriver2.log (3108285 bytes) INFO 2025-06-26 14:44:05,605 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/gps.log (50612 bytes) INFO 2025-06-26 14:44:05,620 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/hydroscatlog.log (2973118 bytes) INFO 2025-06-26 14:44:05,964 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/navigation.log (10411266 bytes) INFO 2025-06-26 14:44:06,862 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/isuslog.log (206197 bytes) INFO 2025-06-26 14:44:06,889 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.113.00/isuslog.log: [1 2 3 4 6 7 8] INFO 2025-06-26 14:44:06,891 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/parosci.log (3624422 bytes) INFO 2025-06-26 14:44:07,238 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/tailCone.log (434107 bytes) INFO 2025-06-26 14:44:07,302 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/biolume.log (2411692 bytes) INFO 2025-06-26 14:44:07,543 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:44:07,700 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.61 seconds INFO 2025-06-26 14:44:07,700 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.113.00/lopc.bin (29908919 bytes) INFO 2025-06-26 14:44:07,701 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:44:07 2025 INFO 2025-06-26 14:44:07,701 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.113.00/parosci.nc INFO 2025-06-26 14:44:07,701 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:44:07,701 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.113.00/parosci.nc INFO 2025-06-26 14:44:07,705 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1240516312.8, sensor_off_time = 1240525167.2 INFO 2025-06-26 14:44:07,705 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 8854 seconds. Expecting to read 17708 L frames from the lopc.bin file. INFO 2025-06-26 14:44:07,705 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 17708 records from the lopc.bin file. INFO 2025-06-26 14:44:07,813 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-04-23 19:51:52 Z and endTime = 2009-04-23 22:19:27 Z with 17708 records expected to be read from lopc.bin INFO 2025-06-26 14:44:07,813 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.113.00/lopc.bin INFO 2025-06-26 14:44:07,813 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.113.00/lopc.nc INFO 2025-06-26 14:44:07,814 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.113.00/lopc.nc INFO 2025-06-26 14:44:07,815 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.113.00 INFO 2025-06-26 14:44:07,815 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:44:07,992 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:44:07,992 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:44:07,992 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 14:44:08,201 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 14:44:08,202 process.py calibrate():227 [1] Calibration steps for 2009.113.00 INFO 2025-06-26 14:44:08,340 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 14:44:08,342 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:44:09,222 calibrate.py _nudge_pos():1806 [1] 118: 0.130 0.0005651 -0.0000378 1515 5.05 16.596 -1.389 2009-04-23T19:58:52.018670848 INFO 2025-06-26 14:44:10,010 calibrate.py _nudge_pos():1806 [1] 196: 0.120 0.0025414 0.0000612 4445 14.81 25.432 0.766 2009-04-23T20:14:58.022494976 INFO 2025-06-26 14:44:10,697 calibrate.py _nudge_pos():1806 [1] 267: 0.130 0.0023347 -0.0001913 3820 12.73 27.190 -2.785 2009-04-23T20:28:52.015362816 INFO 2025-06-26 14:44:11,449 calibrate.py _nudge_pos():1806 [1] 343: 0.140 0.0024257 -0.0001611 3945 13.15 27.359 -2.271 2009-04-23T20:43:16.016174592 INFO 2025-06-26 14:44:12,289 calibrate.py _nudge_pos():1806 [1] 428: 0.120 0.0015778 -0.0001209 3450 11.50 20.352 -1.949 2009-04-23T20:56:10.023151360 INFO 2025-06-26 14:44:12,327 calibrate.py _nudge_pos():1806 [1] 432: 0.130 0.0000121 -0.0000048 35 0.11 15.800 -7.794 2009-04-23T20:56:20.022466304 INFO 2025-06-26 14:44:13,179 calibrate.py _nudge_pos():1806 [1] 518: 0.140 0.0007583 -0.0017263 9515 31.71 3.546 -10.087 2009-04-23T21:29:28.016279552 INFO 2025-06-26 14:44:14,002 calibrate.py _nudge_pos():1806 [1] 603: 0.140 0.0000894 -0.0003689 4440 14.80 0.896 -4.620 2009-04-23T21:45:40.019692544 INFO 2025-06-26 14:44:14,735 calibrate.py _nudge_pos():1806 [1] 675: 0.130 0.0006617 -0.0018265 9635 32.11 3.056 -10.539 2009-04-23T22:18:58.022820352 INFO 2025-06-26 14:44:14,832 calibrate.py _nudge_pos():1806 [1] 685: 0.140 0.0000000 0.0000011 75 0.25 0.002 0.855 2009-04-23T22:19:22.021176064 INFO 2025-06-26 14:44:14,886 calibrate.py _nudge_pos():1862 [1] 657: - - - 1 0.00 - - INFO 2025-06-26 14:44:14,886 calibrate.py _nudge_pos():1868 [1] Points in final series = 44106 INFO 2025-06-26 14:44:14,945 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=30) for self.args.mission=2009.113.00 INFO 2025-06-26 14:44:14,948 calibrate.py _depth_process():2175 [1] Setting 935 depths values to NaN WARNING 2025-06-26 14:44:14,950 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:44:15,437 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:44:15,804 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:44:16,075 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:44:16,078 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.113.00/ctd1.nc INFO 2025-06-26 14:44:16,079 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:44:16,080 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 14:44:16,080 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:44:16,417 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:44:16,690 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:44:16,692 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.113.00/ctd2.nc INFO 2025-06-26 14:44:16,694 calibrate.py _range_qc_combined_nc():898 [1] Setting 172 ctd2_salinity values to NaN INFO 2025-06-26 14:44:16,694 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 14:44:16,694 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:44:17,017 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:44:17,406 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 13620 98100 131100 131101 131102 131103 247500 398880 398881 400320 400321 400322 429540 443880] INFO 2025-06-26 14:44:17,491 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:44:17,497 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 14:44:17,497 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2009.113.00 ERROR 2025-06-26 14:44:17,497 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.113.00 INFO 2025-06-26 14:44:17,508 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_cal.nc INFO 2025-06-26 14:44:17,579 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_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 14:44:17,587 process.py align():251 [1] Alignment steps for 2009.113.00 INFO 2025-06-26 14:44:17,628 align.py process_cal():139 [1] Processing dorado_2009.113.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.113.00 INFO 2025-06-26 14:44:17,649 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:44:17,653 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:44:17,695 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:44:17,700 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:44:17,742 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:44:17,746 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:44:17,770 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:44:17,770 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:44:17,785 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:44:17,790 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:44:17,834 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:17,839 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:17,875 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:17,879 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:17,914 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:17,918 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:17,953 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:17,957 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:17,995 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:17,998 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,034 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,038 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,074 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,078 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,113 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,117 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,154 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,158 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,194 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,198 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,234 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,238 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,272 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,276 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,316 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,320 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,356 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,360 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,396 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,400 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,435 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,440 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,477 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,481 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,516 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,520 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,560 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,565 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,600 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.113.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:44:18,603 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:44:18,649 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:44:18,684 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:44:18,717 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:44:18,755 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:44:18,791 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 14:44:18,807 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_align.nc INFO 2025-06-26 14:44:18,879 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_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 14:44:18,882 process.py resample():273 [1] Resampling steps for 2009.113.00 INFO 2025-06-26 14:44:18,883 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:44:18,912 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_align.nc mission netCDF file INFO 2025-06-26 14:44:18,918 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_align.nc mission netCDF file INFO 2025-06-26 14:44:18,919 resample.py get_mission_start_end():1145 [1] navigation: 2009-04-23T19:52:26.065110528 to 2009-04-23T22:19:27.220819968 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:44:18,921 resample.py get_mission_start_end():1145 [1] hs2 : 2009-04-23T19:51:58.457001984 to 2009-04-23T22:19:27.190822144 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 14:44:18,922 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-04-23T19:52:36.204416000 to 2009-04-23T22:19:27.060830720 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 14:44:18,924 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-04-23T19:52:19.165583104 to 2009-04-23T22:19:27.210820608 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 14:44:18,925 resample.py get_mission_start_end():1145 [1] isus : 2009-04-23T19:52:52.843276032 to 2009-04-23T22:19:27.070830336 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 14:44:18,926 resample.py get_mission_start_end():1145 [1] biolume : 2009-04-23T19:51:52.327387648 to 2009-04-23T22:19:26.320847360 (0 days 00:00:00.899972608 before mission_end) INFO 2025-06-26 14:44:18,928 resample.py get_mission_start_end():1145 [1] tailcone : 2009-04-23T19:51:56.907108096 to 2009-04-23T22:19:26.610861824 (0 days 00:00:00.609958144 before mission_end) INFO 2025-06-26 14:44:18,928 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_align.nc mission netCDF file INFO 2025-06-26 14:44:18,929 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,056 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,082 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,105 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,129 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,151 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,173 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,194 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,216 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,236 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,256 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,276 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,297 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,317 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,337 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,357 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,377 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,400 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,423 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,447 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,470 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,493 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,516 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,531 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,546 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,559 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,576 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,591 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:44:19,746 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_1S.nc INFO 2025-06-26 14:44:21,473 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 14:44:27,737 create_products.py gulper_odv():522 [1] Wrote 6 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.113.00/dorado_2009.113.00_1S_Gulper.txt INFO 2025-06-26 14:44:27,737 process.py archive():337 [1] Archiving steps for 2009.113.00 INFO 2025-06-26 14:44:27,737 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00, BASE_PATH = /data/auv_data INFO 2025-06-26 14:44:27,738 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 14:44:27,739 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.113.00_1S.nc INFO 2025-06-26 14:44:27,752 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:44:27,753 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.113.00_cal.nc INFO 2025-06-26 14:44:27,794 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:44:27,796 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.113.00_align.nc INFO 2025-06-26 14:44:27,836 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:44:27,852 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,865 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,870 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,883 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,917 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,924 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,940 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,947 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,975 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,981 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009113/2009.113.00 done. INFO 2025-06-26 14:44:27,981 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:44:27,982 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.113.00_1S_Gulper.txt INFO 2025-06-26 14:44:27,987 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.113.00/dorado_2009.113.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 14:44:27,987 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.113.00/dorado_2009.113.00_processing.log /Volumes/AUVCTD/surveys/2009/netcdf