INFO 2025-06-26 19:28:31,218 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 19:28:31,218 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - inbound mission, Gulper 0 fired on .01 mission and Gulpers 1 through 6 fired on .02 - ctdToUse = ctd1 INFO 2025-06-26 19:28:31,218 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.076.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:28:31,218 process.py download_process():165 [1] Download and processing steps for 2013.076.01 INFO 2025-06-26 19:28:31,218 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013076/2013.076.01 INFO 2025-06-26 19:28:31,218 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013076/2013.076.01 to /data/auv_data/dorado/missionlogs/2013.076.01 INFO 2025-06-26 19:28:32,300 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.076.01 INFO 2025-06-26 19:28:32,300 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/ctdDriver.log (1122918 bytes) INFO 2025-06-26 19:28:32,384 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/ctdDriver2.log (1122815 bytes) INFO 2025-06-26 19:28:32,470 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/gps.log (35708 bytes) INFO 2025-06-26 19:28:32,482 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/hydroscatlog.log (986938 bytes) INFO 2025-06-26 19:28:32,592 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/navigation.log (3950118 bytes) INFO 2025-06-26 19:28:32,893 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/isuslog.log (85621 bytes) INFO 2025-06-26 19:28:32,906 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/parosci.log (1170182 bytes) INFO 2025-06-26 19:28:33,009 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/tailCone.log (706171 bytes) INFO 2025-06-26 19:28:33,103 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/biolume.log (824306 bytes) INFO 2025-06-26 19:28:33,186 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:28:33,234 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.93 seconds INFO 2025-06-26 19:28:33,234 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.01/lopc.bin (5708499 bytes) INFO 2025-06-26 19:28:33,234 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:28:33 2025 INFO 2025-06-26 19:28:33,234 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.076.01/parosci.nc INFO 2025-06-26 19:28:33,234 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:28:33,234 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.076.01/parosci.nc INFO 2025-06-26 19:28:33,236 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363534886.5, sensor_off_time = 1363537827.5 INFO 2025-06-26 19:28:33,237 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 2941 seconds. Expecting to read 5882 L frames from the lopc.bin file. INFO 2025-06-26 19:28:33,237 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 5882 records from the lopc.bin file. INFO 2025-06-26 19:28:33,272 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-17 15:41:26 Z and endTime = 2013-03-17 16:30:27 Z with 5882 records expected to be read from lopc.bin INFO 2025-06-26 19:28:33,272 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.076.01/lopc.bin INFO 2025-06-26 19:28:33,272 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.076.01/lopc.nc INFO 2025-06-26 19:28:33,272 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.076.01/lopc.nc INFO 2025-06-26 19:28:33,273 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.076.01 INFO 2025-06-26 19:28:33,273 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:28:33,276 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0147257 WARNING 2025-06-26 19:28:33,276 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:28:33,328 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:28:33,328 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:28:33,328 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:28:33,639 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:28:33,639 process.py calibrate():227 [1] Calibration steps for 2013.076.01 INFO 2025-06-26 19:28:33,724 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 19:28:33,726 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:28:34,305 calibrate.py _nudge_pos():1806 [1] 93: 0.140 0.0019509 -0.0015455 2188 7.30 41.305 -39.249 2013-03-17T15:50:15.929122048 INFO 2025-06-26 19:28:34,849 calibrate.py _nudge_pos():1806 [1] 152: 0.150 0.0120968 -0.0055360 9790 32.63 57.263 -31.438 2013-03-17T16:23:51.931016448 INFO 2025-06-26 19:28:35,674 calibrate.py _nudge_pos():1806 [1] 241: 0.150 0.0001245 -0.0000321 140 0.46 41.520 -12.829 2013-03-17T16:25:47.923070464 INFO 2025-06-26 19:28:35,712 calibrate.py _nudge_pos():1806 [1] 245: 0.150 0.0000852 -0.0000140 70 0.23 57.208 -11.276 2013-03-17T16:26:04.931905280 INFO 2025-06-26 19:28:36,035 calibrate.py _nudge_pos():1806 [1] 280: 0.150 0.0000759 -0.0000238 65 0.21 54.929 -20.694 2013-03-17T16:26:51.928685824 INFO 2025-06-26 19:28:37,816 calibrate.py _nudge_pos():1806 [1] 472: 0.150 0.0000617 -0.0000150 60 0.20 48.460 -14.163 2013-03-17T16:30:15.924710912 INFO 2025-06-26 19:28:37,922 calibrate.py _nudge_pos():1862 [1] 446: - - - 3 0.01 - - INFO 2025-06-26 19:28:37,922 calibrate.py _nudge_pos():1868 [1] Points in final series = 14514 WARNING 2025-06-26 19:28:37,944 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:28:38,066 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:38,195 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:38,288 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:38,290 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.076.01/ctd1.nc INFO 2025-06-26 19:28:38,291 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:28:38,291 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 19:28:38,291 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:28:38,412 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:38,502 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:28:38,503 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.076.01/ctd2.nc INFO 2025-06-26 19:28:38,504 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:28:38,505 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 19:28:38,505 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:28:38,515 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:28:38,666 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:28:38,679 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.076.01 ERROR 2025-06-26 19:28:38,679 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.076.01 INFO 2025-06-26 19:28:38,694 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_cal.nc INFO 2025-06-26 19:28:38,751 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 19:28:38,757 process.py align():251 [1] Alignment steps for 2013.076.01 INFO 2025-06-26 19:28:38,783 align.py process_cal():139 [1] Processing dorado_2013.076.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.076.01 INFO 2025-06-26 19:28:38,791 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:38,793 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:38,812 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:38,814 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:38,831 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:38,833 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:38,843 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:28:38,844 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:28:38,851 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:28:38,853 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:38,870 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,872 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:38,889 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,891 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:38,907 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,910 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:38,926 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,928 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:38,944 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,946 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:38,962 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,964 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:38,981 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:38,983 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,000 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,081 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,098 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,100 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,117 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,119 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,135 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,138 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,154 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,156 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,173 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,175 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,192 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,194 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,211 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,213 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,230 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,232 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,249 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,252 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,269 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,271 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,291 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,308 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,310 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,327 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,329 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,346 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:28:39,348 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:28:39,370 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:28:39,389 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:28:39,407 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:28:39,426 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:28:39,446 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:28:39,469 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:28:39,559 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:28:39,575 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_align.nc INFO 2025-06-26 19:28:39,637 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 19:28:39,639 process.py resample():273 [1] Resampling steps for 2013.076.01 INFO 2025-06-26 19:28:39,640 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:28:39,665 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_align.nc mission netCDF file INFO 2025-06-26 19:28:39,670 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_align.nc mission netCDF file INFO 2025-06-26 19:28:39,671 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-17T15:42:04.542784256 to 2013-03-17T16:30:27.523916544 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:28:39,673 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-17T15:41:31.885021440 to 2013-03-17T16:30:27.473919744 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 19:28:39,674 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-17T15:41:45.434093568 to 2013-03-17T16:30:27.473919744 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 19:28:39,675 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-17T15:41:45.444092672 to 2013-03-17T16:30:27.333929472 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 19:28:39,677 resample.py get_mission_start_end():1145 [1] isus : 2013-03-17T15:42:41.550249216 to 2013-03-17T16:30:26.633977344 (0 days 00:00:00.889939200 before mission_end) INFO 2025-06-26 19:28:39,678 resample.py get_mission_start_end():1145 [1] biolume : 2013-03-17T15:41:25.735408640 to 2013-03-17T16:30:26.073981440 (0 days 00:00:01.449935104 before mission_end) INFO 2025-06-26 19:28:39,679 resample.py get_mission_start_end():1145 [1] tailcone : 2013-03-17T15:41:27.435326464 to 2013-03-17T16:30:27.433922816 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 19:28:39,680 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_align.nc mission netCDF file INFO 2025-06-26 19:28:39,680 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,736 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,750 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,762 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,774 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,786 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,798 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,809 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,820 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,831 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,841 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,851 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,861 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,871 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,881 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,891 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,901 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,911 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,923 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,934 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,946 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,958 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,968 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,979 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:39,990 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,000 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,011 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,021 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,030 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,037 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,041 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:28:40,041 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:28:40,144 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:28:40,164 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:28:40,177 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:28:40,183 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:28:40,190 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:28:40,190 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:28:40,207 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:28:40,332 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_1S.nc INFO 2025-06-26 19:28:43,501 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:28:43,668 create_products.py gulper_odv():522 [1] Wrote 1 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.076.01/dorado_2013.076.01_1S_Gulper.txt INFO 2025-06-26 19:28:43,668 process.py archive():337 [1] Archiving steps for 2013.076.01 INFO 2025-06-26 19:28:43,668 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:28:43,669 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:28:43,670 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.076.01_1S.nc INFO 2025-06-26 19:28:43,678 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:28:43,679 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.076.01_cal.nc INFO 2025-06-26 19:28:43,703 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:28:43,705 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.076.01_align.nc INFO 2025-06-26 19:28:43,739 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:28:43,752 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,762 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,767 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,776 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,793 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,799 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,808 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,818 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,833 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,839 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.01 done. INFO 2025-06-26 19:28:43,839 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:28:43,840 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.076.01_1S_Gulper.txt INFO 2025-06-26 19:28:43,846 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.076.01/dorado_2013.076.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:28:43,846 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.01/dorado_2013.076.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf