INFO 2025-06-26 19:49:10,744 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 19:49:10,744 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:49:10,744 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.273.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:49:10,744 process.py download_process():165 [1] Download and processing steps for 2013.273.00 INFO 2025-06-26 19:49:10,744 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013273/2013.273.00 INFO 2025-06-26 19:49:10,744 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013273/2013.273.00 to /data/auv_data/dorado/missionlogs/2013.273.00 INFO 2025-06-26 19:49:15,819 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.273.00 INFO 2025-06-26 19:49:15,819 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/ctdDriver.log (9174534 bytes) INFO 2025-06-26 19:49:16,492 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/ctdDriver2.log (9180959 bytes) INFO 2025-06-26 19:49:17,154 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/gps.log (94460 bytes) INFO 2025-06-26 19:49:17,172 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/hydroscatlog.log (8037058 bytes) INFO 2025-06-26 19:49:17,998 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/navigation.log (32500054 bytes) INFO 2025-06-26 19:49:20,299 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/isuslog.log (733493 bytes) INFO 2025-06-26 19:49:20,374 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/parosci.log (11279750 bytes) INFO 2025-06-26 19:49:21,317 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/tailCone.log (5744155 bytes) INFO 2025-06-26 19:49:22,016 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/biolume.log (6686066 bytes) INFO 2025-06-26 19:49:22,676 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:49:23,009 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.19 seconds INFO 2025-06-26 19:49:23,009 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.273.00/lopc.bin (68557171 bytes) INFO 2025-06-26 19:49:23,009 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:49:23 2025 INFO 2025-06-26 19:49:23,009 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.273.00/parosci.nc INFO 2025-06-26 19:49:23,009 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:49:23,009 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.273.00/parosci.nc INFO 2025-06-26 19:49:23,013 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1380555303.5, sensor_off_time = 1380579235.6 INFO 2025-06-26 19:49:23,013 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 23932 seconds. Expecting to read 47864 L frames from the lopc.bin file. INFO 2025-06-26 19:49:23,013 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 47864 records from the lopc.bin file. INFO 2025-06-26 19:49:23,292 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-09-30 15:35:03 Z and endTime = 2013-09-30 22:13:55 Z with 47864 records expected to be read from lopc.bin INFO 2025-06-26 19:49:23,292 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.273.00/lopc.bin INFO 2025-06-26 19:49:23,292 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.273.00/lopc.nc INFO 2025-06-26 19:49:23,293 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.273.00/lopc.nc INFO 2025-06-26 19:49:23,293 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.273.00 INFO 2025-06-26 19:49:23,293 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:49:23,326 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:49:23,326 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:49:23,326 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:49:28,200 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:49:28,202 process.py calibrate():227 [1] Calibration steps for 2013.273.00 INFO 2025-06-26 19:49:28,479 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 19:49:28,481 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:49:29,453 calibrate.py _nudge_pos():1806 [1] 131: 0.160 0.0004398 -0.0010594 1335 4.45 14.692 -44.146 2013-09-30T15:41:39.500704256 INFO 2025-06-26 19:49:30,367 calibrate.py _nudge_pos():1806 [1] 227: 0.170 0.0022970 -0.0042759 8345 27.81 12.265 -28.488 2013-09-30T16:11:03.499862016 INFO 2025-06-26 19:49:31,195 calibrate.py _nudge_pos():1806 [1] 315: 0.170 0.0011819 -0.0037784 9075 30.25 5.802 -23.148 2013-09-30T16:42:45.499566080 INFO 2025-06-26 19:49:32,017 calibrate.py _nudge_pos():1806 [1] 402: 0.170 0.0009537 -0.0046897 9560 31.86 4.443 -27.273 2013-09-30T17:16:03.502693376 INFO 2025-06-26 19:49:32,047 calibrate.py _nudge_pos():1806 [1] 405: 0.170 -0.0000722 -0.0001530 220 0.73 -14.683 -38.851 2013-09-30T17:16:49.499542528 INFO 2025-06-26 19:49:32,945 calibrate.py _nudge_pos():1806 [1] 499: 0.170 0.0007212 -0.0043164 9355 31.18 3.433 -25.652 2013-09-30T17:49:33.504998912 INFO 2025-06-26 19:49:33,807 calibrate.py _nudge_pos():1806 [1] 589: 0.180 0.0021499 -0.0043230 11435 38.11 8.369 -21.018 2013-09-30T18:29:09.502232064 INFO 2025-06-26 19:49:34,550 calibrate.py _nudge_pos():1806 [1] 666: 0.200 0.0007748 -0.0007626 5920 19.73 5.826 -7.162 2013-09-30T18:50:09.495916544 INFO 2025-06-26 19:49:34,896 calibrate.py _nudge_pos():1806 [1] 702: 0.190 0.0003018 -0.0012357 6515 21.71 2.062 -10.546 2013-09-30T19:12:27.504256768 INFO 2025-06-26 19:49:35,706 calibrate.py _nudge_pos():1806 [1] 786: 0.200 0.0019201 -0.0028111 14195 47.31 6.018 -11.010 2013-09-30T20:01:09.504086016 INFO 2025-06-26 19:49:36,465 calibrate.py _nudge_pos():1806 [1] 863: 0.010 0.0013292 -0.0022167 9640 32.13 6.134 -12.784 2013-09-30T20:34:33.696789248 INFO 2025-06-26 19:49:37,222 calibrate.py _nudge_pos():1806 [1] 941: 0.010 0.0010736 -0.0014842 7355 24.51 6.492 -11.219 2013-09-30T21:00:21.700743936 INFO 2025-06-26 19:49:37,326 calibrate.py _nudge_pos():1806 [1] 951: 0.010 -0.0000060 0.0000275 80 0.26 -3.404 19.332 2013-09-30T21:00:46.699031296 INFO 2025-06-26 19:49:38,064 calibrate.py _nudge_pos():1806 [1] 1026: 0.010 -0.0000639 -0.0000008 45 0.15 -64.628 -1.040 2013-09-30T21:02:09.703345152 INFO 2025-06-26 19:49:38,104 calibrate.py _nudge_pos():1806 [1] 1030: 0.020 0.0009995 -0.0017845 7545 25.15 5.891 -13.150 2013-09-30T21:27:21.699766272 INFO 2025-06-26 19:49:39,035 calibrate.py _nudge_pos():1806 [1] 1126: 0.010 0.0011916 -0.0016231 9395 31.31 5.638 -9.605 2013-09-30T22:00:15.704537600 INFO 2025-06-26 19:49:39,931 calibrate.py _nudge_pos():1806 [1] 1218: 0.020 0.0005602 -0.0004673 3235 10.78 7.699 -8.032 2013-09-30T22:12:33.703981056 INFO 2025-06-26 19:49:40,731 calibrate.py _nudge_pos():1862 [1] 1263: - - - 4 0.01 - - INFO 2025-06-26 19:49:40,731 calibrate.py _nudge_pos():1868 [1] Points in final series = 119367 INFO 2025-06-26 19:49:41,088 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 5 of 95667 INFO 2025-06-26 19:49:41,820 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:49:42,704 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:49:43,422 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:49:43,425 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.273.00/ctd1.nc INFO 2025-06-26 19:49:43,426 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:49:43,426 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 19:49:43,426 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:49:44,263 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:49:44,968 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:49:44,971 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.273.00/ctd2.nc INFO 2025-06-26 19:49:44,972 calibrate.py _range_qc_combined_nc():898 [1] Setting 204 ctd2_salinity values to NaN INFO 2025-06-26 19:49:44,973 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 19:49:44,973 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:49:45,026 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:49:46,091 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63] INFO 2025-06-26 19:49:46,299 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:50:07,830 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.273.00 ERROR 2025-06-26 19:50:07,830 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.273.00 INFO 2025-06-26 19:50:07,923 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_cal.nc INFO 2025-06-26 19:50:08,085 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 19:50:08,091 process.py align():251 [1] Alignment steps for 2013.273.00 INFO 2025-06-26 19:50:08,134 align.py process_cal():139 [1] Processing dorado_2013.273.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.273.00 INFO 2025-06-26 19:50:08,168 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:08,172 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:08,249 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:08,255 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:08,333 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:08,339 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:08,385 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:50:08,385 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:50:08,415 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:08,421 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:08,496 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,501 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,567 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,571 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,637 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,642 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,708 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,712 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,781 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,785 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,851 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,856 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,923 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,928 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:08,995 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:08,999 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,067 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,072 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,139 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,145 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,213 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,218 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,284 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,290 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,358 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,362 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,429 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,434 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,501 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,506 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,573 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,578 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,646 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,651 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,721 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,726 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,795 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,800 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,868 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,873 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:09,941 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:09,946 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:10,015 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.273.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:10,019 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:10,106 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:50:10,168 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:50:10,228 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:50:10,292 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:50:10,355 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:50:10,464 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:50:11,068 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:11,124 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_align.nc INFO 2025-06-26 19:50:11,290 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 19:50:11,293 process.py resample():273 [1] Resampling steps for 2013.273.00 INFO 2025-06-26 19:50:11,293 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:50:11,332 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_align.nc mission netCDF file INFO 2025-06-26 19:50:11,338 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_align.nc mission netCDF file INFO 2025-06-26 19:50:11,340 resample.py get_mission_start_end():1145 [1] navigation: 2013-09-30T15:35:39.905338368 to 2013-09-30T22:13:55.498377984 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 19:50:11,342 resample.py get_mission_start_end():1145 [1] hs2 : 2013-09-30T15:35:08.427494400 to 2013-09-30T22:13:55.428382720 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 19:50:11,344 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-09-30T15:35:46.054916864 to 2013-09-30T22:13:55.518376704 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 19:50:11,345 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-09-30T15:35:29.176073216 to 2013-09-30T22:13:55.398384896 (0 days 00:00:00.219984896 before mission_end) INFO 2025-06-26 19:50:11,347 resample.py get_mission_start_end():1145 [1] isus : 2013-09-30T15:36:20.152580864 to 2013-09-30T22:13:55.618369792 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:50:11,348 resample.py get_mission_start_end():1145 [1] biolume : 2013-09-30T15:35:02.047897344 to 2013-09-30T22:13:54.708397824 (0 days 00:00:00.909971968 before mission_end) INFO 2025-06-26 19:50:11,350 resample.py get_mission_start_end():1145 [1] tailcone : 2013-09-30T15:35:03.607824896 to 2013-09-30T22:13:55.618369792 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:50:11,350 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_align.nc mission netCDF file INFO 2025-06-26 19:50:11,351 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,604 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,648 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,691 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,735 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,773 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,810 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,847 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,884 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,918 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,952 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:11,985 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,019 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,055 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,090 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,123 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,156 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,189 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,225 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,261 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,301 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,338 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,375 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,412 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,448 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,467 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,483 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,499 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,513 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,527 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:12,531 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:50:12,532 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:50:13,386 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:50:13,541 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:50:13,623 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:50:13,660 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:50:13,689 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:50:13,689 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:50:13,736 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:13,986 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_1S.nc INFO 2025-06-26 19:50:15,919 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:50:26,615 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.273.00/dorado_2013.273.00_1S_Gulper.txt INFO 2025-06-26 19:50:26,615 process.py archive():337 [1] Archiving steps for 2013.273.00 INFO 2025-06-26 19:50:26,615 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:50:26,616 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:50:26,617 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.273.00_1S.nc INFO 2025-06-26 19:50:26,640 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:50:26,641 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.273.00_cal.nc INFO 2025-06-26 19:50:26,794 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:50:26,794 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.273.00_align.nc INFO 2025-06-26 19:50:27,020 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:50:27,050 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,077 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,081 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,105 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,194 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,203 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,235 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,259 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,330 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,346 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013273/2013.273.00 done. INFO 2025-06-26 19:50:27,346 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:50:27,347 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.273.00_1S_Gulper.txt INFO 2025-06-26 19:50:27,352 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.273.00/dorado_2013.273.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:50:27,352 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.273.00/dorado_2013.273.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf