INFO 2025-06-26 20:17:18,026 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:17:18,026 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:17:18,026 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.103.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:17:18,026 process.py download_process():165 [1] Download and processing steps for 2014.103.00 INFO 2025-06-26 20:17:18,026 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014103/2014.103.00 INFO 2025-06-26 20:17:18,026 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014103/2014.103.00 to /data/auv_data/dorado/missionlogs/2014.103.00 INFO 2025-06-26 20:17:21,222 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.103.00 INFO 2025-06-26 20:17:21,223 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/ctdDriver.log (4436838 bytes) INFO 2025-06-26 20:17:21,551 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/ctdDriver2.log (4443455 bytes) INFO 2025-06-26 20:17:21,871 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/gps.log (69260 bytes) INFO 2025-06-26 20:17:21,887 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/hydroscatlog.log (3893338 bytes) INFO 2025-06-26 20:17:22,284 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/navigation.log (16631874 bytes) INFO 2025-06-26 20:17:23,504 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/isuslog.log (287797 bytes) INFO 2025-06-26 20:17:23,536 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/parosci.log (5465942 bytes) INFO 2025-06-26 20:17:23,997 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/tailCone.log (2783275 bytes) INFO 2025-06-26 20:17:24,341 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/biolume.log (3241146 bytes) INFO 2025-06-26 20:17:24,658 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:17:24,821 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.60 seconds INFO 2025-06-26 20:17:24,822 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.103.00/lopc.bin (40293143 bytes) INFO 2025-06-26 20:17:24,822 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:17:24 2025 INFO 2025-06-26 20:17:24,822 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.103.00/parosci.nc INFO 2025-06-26 20:17:24,822 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:17:24,822 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.103.00/parosci.nc INFO 2025-06-26 20:17:24,825 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397401113.4, sensor_off_time = 1397412707.5 INFO 2025-06-26 20:17:24,825 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11594 seconds. Expecting to read 23188 L frames from the lopc.bin file. INFO 2025-06-26 20:17:24,825 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 23188 records from the lopc.bin file. INFO 2025-06-26 20:17:24,963 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-13 14:58:33 Z and endTime = 2014-04-13 18:11:47 Z with 23188 records expected to be read from lopc.bin INFO 2025-06-26 20:17:24,963 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.103.00/lopc.bin INFO 2025-06-26 20:17:24,964 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.103.00/lopc.nc INFO 2025-06-26 20:17:24,964 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.103.00/lopc.nc INFO 2025-06-26 20:17:24,964 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.103.00 INFO 2025-06-26 20:17:24,965 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:17:25,054 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:17:25,054 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:17:25,054 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:17:25,192 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:17:25,193 process.py calibrate():227 [1] Calibration steps for 2014.103.00 INFO 2025-06-26 20:17:25,328 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:17:25,330 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:17:26,044 calibrate.py _nudge_pos():1806 [1] 115: 0.110 -0.0008889 0.0003617 1635 5.45 -25.213 12.305 2014-04-13T15:05:52.088947968 INFO 2025-06-26 20:17:26,565 calibrate.py _nudge_pos():1806 [1] 171: 0.110 -0.0079125 0.0021275 9895 32.98 -37.054 11.954 2014-04-13T15:39:46.089609472 INFO 2025-06-26 20:17:27,025 calibrate.py _nudge_pos():1806 [1] 220: 0.110 -0.0084542 0.0028163 9960 33.20 -39.321 15.720 2014-04-13T16:13:46.089859840 INFO 2025-06-26 20:17:27,552 calibrate.py _nudge_pos():1806 [1] 277: 0.120 -0.0061249 0.0023832 9948 33.16 -28.509 13.316 2014-04-13T16:47:52.089699328 INFO 2025-06-26 20:17:28,086 calibrate.py _nudge_pos():1806 [1] 334: 0.120 -0.0039678 0.0014462 9590 31.96 -19.158 8.384 2014-04-13T17:20:46.094470656 INFO 2025-06-26 20:17:28,628 calibrate.py _nudge_pos():1806 [1] 392: 0.130 -0.0035445 0.0015623 9345 31.15 -17.560 9.294 2014-04-13T17:52:52.092530688 INFO 2025-06-26 20:17:29,163 calibrate.py _nudge_pos():1806 [1] 449: 0.130 -0.0012977 0.0006327 2840 9.46 -21.159 12.388 2014-04-13T18:03:16.089783808 INFO 2025-06-26 20:17:29,193 calibrate.py _nudge_pos():1806 [1] 452: 0.130 -0.0000746 -0.0000741 60 0.20 -58.505 -69.825 2014-04-13T18:03:30.088825088 INFO 2025-06-26 20:17:33,881 calibrate.py _nudge_pos():1862 [1] 902: - - - 2 0.00 - - INFO 2025-06-26 20:17:33,881 calibrate.py _nudge_pos():1868 [1] Points in final series = 57740 INFO 2025-06-26 20:17:34,400 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:17:34,842 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:17:35,186 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:17:35,188 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.103.00/ctd1.nc INFO 2025-06-26 20:17:35,189 calibrate.py _range_qc_combined_nc():898 [1] Setting 125 ctd1_salinity values to NaN INFO 2025-06-26 20:17:35,190 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:17:35,190 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:17:35,603 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:17:35,946 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:17:35,948 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.103.00/ctd2.nc INFO 2025-06-26 20:17:35,950 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:17:35,950 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:17:35,950 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:17:35,972 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:17:36,457 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64] INFO 2025-06-26 20:17:36,559 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:17:46,943 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.103.00 ERROR 2025-06-26 20:17:46,944 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.103.00 INFO 2025-06-26 20:17:46,990 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_cal.nc INFO 2025-06-26 20:17:47,089 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:17:47,095 process.py align():251 [1] Alignment steps for 2014.103.00 INFO 2025-06-26 20:17:47,126 align.py process_cal():139 [1] Processing dorado_2014.103.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.103.00 INFO 2025-06-26 20:17:47,145 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:47,148 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:47,191 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:47,194 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:47,236 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:47,239 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:47,264 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:17:47,264 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:17:47,281 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:17:47,284 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:47,327 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,330 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,366 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,369 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,407 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,410 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,447 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,450 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,487 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,490 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,527 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,530 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,568 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,571 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,608 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,611 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,649 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,652 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,689 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,692 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,731 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,734 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,772 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,775 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,814 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,817 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,854 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,857 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,896 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,899 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,937 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,940 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:47,979 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:47,982 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:48,018 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:48,022 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:48,060 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:48,064 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:48,102 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:48,105 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:48,144 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:48,147 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:48,185 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.103.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:17:48,188 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:17:48,235 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:17:48,270 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:17:48,305 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:17:48,340 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:17:48,378 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:17:48,434 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:17:48,728 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:17:48,761 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_align.nc INFO 2025-06-26 20:17:48,865 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:17:48,868 process.py resample():273 [1] Resampling steps for 2014.103.00 INFO 2025-06-26 20:17:48,868 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:17:48,899 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_align.nc mission netCDF file INFO 2025-06-26 20:17:48,904 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_align.nc mission netCDF file INFO 2025-06-26 20:17:48,905 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-13T14:59:19.145866496 to 2014-04-13T18:11:47.494750208 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 20:17:48,907 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-13T14:58:38.078679808 to 2014-04-13T18:11:47.414755840 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 20:17:48,908 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-13T14:59:15.126141696 to 2014-04-13T18:11:47.364759296 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 20:17:48,909 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-13T14:58:58.217300224 to 2014-04-13T18:11:47.454753280 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 20:17:48,911 resample.py get_mission_start_end():1145 [1] isus : 2014-04-13T14:59:46.663981312 to 2014-04-13T18:11:46.754801152 (0 days 00:00:00.769947136 before mission_end) INFO 2025-06-26 20:17:48,912 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-13T14:58:30.909136640 to 2014-04-13T18:11:46.064814080 (0 days 00:00:01.459934208 before mission_end) INFO 2025-06-26 20:17:48,913 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-13T14:58:32.899034624 to 2014-04-13T18:11:47.524748288 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:17:48,914 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_align.nc mission netCDF file INFO 2025-06-26 20:17:48,915 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,114 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,138 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,162 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,185 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,207 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,229 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,249 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,270 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,289 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,310 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,329 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,348 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,367 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,387 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,406 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,425 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,444 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,466 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,488 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,509 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,530 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,550 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,571 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,592 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,604 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,616 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,627 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,637 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,647 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:49,651 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:17:49,651 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:17:50,068 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:17:50,141 resample.py add_biolume_proxies():633 [1] Zero flow values found: 11597 of 11597 - replaced with 350 ml/s INFO 2025-06-26 20:17:50,142 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:17:50,183 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:17:50,202 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:17:50,218 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:17:50,219 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:17:50,248 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:17:50,424 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_1S.nc INFO 2025-06-26 20:17:52,076 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:18:00,910 create_products.py gulper_odv():522 [1] Wrote 8 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.103.00/dorado_2014.103.00_1S_Gulper.txt INFO 2025-06-26 20:18:00,910 process.py archive():337 [1] Archiving steps for 2014.103.00 INFO 2025-06-26 20:18:00,910 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:18:00,911 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:18:00,912 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.103.00_1S.nc INFO 2025-06-26 20:18:00,927 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:18:00,928 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.103.00_cal.nc INFO 2025-06-26 20:18:01,011 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:18:01,012 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.103.00_align.nc INFO 2025-06-26 20:18:01,124 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:18:01,141 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,156 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,161 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,175 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,217 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,222 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,242 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,255 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,286 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,292 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014103/2014.103.00 done. INFO 2025-06-26 20:18:01,292 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:18:01,293 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.103.00_1S_Gulper.txt INFO 2025-06-26 20:18:01,297 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.103.00/dorado_2014.103.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:18:01,297 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.103.00/dorado_2014.103.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf