INFO 2025-06-26 20:38:27,144 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 20:38:27,144 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB September 2014 with rhodamine sensor on ctdDriver2, channel 1 - ctdToUse = ctd1 INFO 2025-06-26 20:38:27,144 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.282.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:38:27,144 process.py download_process():165 [1] Download and processing steps for 2014.282.03 INFO 2025-06-26 20:38:27,144 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014282/2014.282.03 INFO 2025-06-26 20:38:27,145 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014282/2014.282.03 to /data/auv_data/dorado/missionlogs/2014.282.03 INFO 2025-06-26 20:38:29,010 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.282.03 INFO 2025-06-26 20:38:29,011 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/ctdDriver.log (1789446 bytes) INFO 2025-06-26 20:38:29,138 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/ctdDriver2.log (1789347 bytes) INFO 2025-06-26 20:38:29,268 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/gps.log (34916 bytes) INFO 2025-06-26 20:38:29,279 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/hydroscatlog.log (1573006 bytes) INFO 2025-06-26 20:38:29,451 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/navigation.log (6692994 bytes) INFO 2025-06-26 20:38:29,958 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/isuslog.log (114933 bytes) INFO 2025-06-26 20:38:29,974 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/parosci.log (2208374 bytes) INFO 2025-06-26 20:38:30,162 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.282.03/parosci.log: [1 2 3] INFO 2025-06-26 20:38:30,169 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/tailCone.log (1126267 bytes) INFO 2025-06-26 20:38:30,345 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/biolume.log (1312502 bytes) INFO 2025-06-26 20:38:30,530 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:38:30,646 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.64 seconds INFO 2025-06-26 20:38:30,646 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.282.03/lopc.bin (8499509 bytes) INFO 2025-06-26 20:38:30,646 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:38:30 2025 INFO 2025-06-26 20:38:30,647 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.282.03/parosci.nc INFO 2025-06-26 20:38:30,647 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:38:30,647 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.282.03/parosci.nc INFO 2025-06-26 20:38:30,650 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1412880301.6, sensor_off_time = 1412884988.5 INFO 2025-06-26 20:38:30,651 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 4686 seconds. Expecting to read 9372 L frames from the lopc.bin file. INFO 2025-06-26 20:38:30,651 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 9372 records from the lopc.bin file. INFO 2025-06-26 20:38:30,709 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-10-09 18:45:01 Z and endTime = 2014-10-09 20:03:08 Z with 9372 records expected to be read from lopc.bin INFO 2025-06-26 20:38:30,709 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.282.03/lopc.bin INFO 2025-06-26 20:38:30,709 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.282.03/lopc.nc INFO 2025-06-26 20:38:30,710 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.282.03/lopc.nc INFO 2025-06-26 20:38:30,711 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.282.03 INFO 2025-06-26 20:38:30,711 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:38:30,713 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:38:30,806 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:38:30,806 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:38:30,806 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:38:31,423 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:38:31,424 process.py calibrate():227 [1] Calibration steps for 2014.282.03 INFO 2025-06-26 20:38:31,528 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 20:38:31,530 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:38:32,589 calibrate.py _nudge_pos():1806 [1] 142: 0.170 -0.0000576 -0.0008933 2150 7.16 -1.193 -23.108 2014-10-09T18:54:27.916258816 INFO 2025-06-26 20:38:33,433 calibrate.py _nudge_pos():1806 [1] 214: 0.180 0.0033507 -0.0028568 7205 24.01 20.682 -22.045 2014-10-09T19:19:39.912680192 INFO 2025-06-26 20:38:34,279 calibrate.py _nudge_pos():1806 [1] 289: 0.170 -0.0034168 -0.0005949 5030 16.76 -30.213 -6.576 2014-10-09T19:37:39.918694400 INFO 2025-06-26 20:38:35,905 calibrate.py _nudge_pos():1806 [1] 426: 0.170 0.0025505 -0.0028180 6730 22.43 16.854 -23.280 2014-10-09T20:02:21.917170688 INFO 2025-06-26 20:38:36,610 calibrate.py _nudge_pos():1862 [1] 428: - - - 3 0.01 - - INFO 2025-06-26 20:38:36,610 calibrate.py _nudge_pos():1868 [1] Points in final series = 23231 INFO 2025-06-26 20:38:37,686 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 2 of 18714 INFO 2025-06-26 20:38:37,907 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:38:38,164 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:38:38,409 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:38:38,411 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.282.03/ctd1.nc INFO 2025-06-26 20:38:38,412 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:38:38,412 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 20:38:38,412 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:38:38,595 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:38:38,736 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:38:38,738 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.282.03/ctd2.nc INFO 2025-06-26 20:38:38,739 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:38:38,739 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 20:38:38,739 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:38:38,752 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:38:38,982 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75] INFO 2025-06-26 20:38:39,053 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:38:44,485 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.282.03 ERROR 2025-06-26 20:38:44,486 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.282.03 INFO 2025-06-26 20:38:44,520 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_cal.nc INFO 2025-06-26 20:38:44,622 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 20:38:44,631 process.py align():251 [1] Alignment steps for 2014.282.03 INFO 2025-06-26 20:38:44,674 align.py process_cal():139 [1] Processing dorado_2014.282.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.282.03 INFO 2025-06-26 20:38:44,691 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:38:44,694 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:38:44,736 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:38:44,740 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:38:44,778 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:38:44,782 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:38:44,804 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:38:44,804 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:38:44,820 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:38:44,824 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:38:44,861 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:44,865 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:44,901 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:44,905 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:44,930 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:44,933 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:44,955 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:44,958 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:44,980 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:44,983 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,005 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,009 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,031 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,034 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,057 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,060 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,082 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,085 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,107 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,110 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,133 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,135 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,157 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,160 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,183 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,186 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,209 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,211 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,235 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,239 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,262 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,265 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,301 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,304 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,335 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,340 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,376 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,380 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,404 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,407 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,429 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,432 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,456 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.282.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:38:45,458 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:38:45,485 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:38:45,508 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:38:45,529 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:38:45,553 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:38:45,585 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:38:45,625 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:38:45,771 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:38:45,798 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_align.nc INFO 2025-06-26 20:38:45,900 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 20:38:45,902 process.py resample():273 [1] Resampling steps for 2014.282.03 INFO 2025-06-26 20:38:45,903 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:38:45,944 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_align.nc mission netCDF file INFO 2025-06-26 20:38:45,952 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_align.nc mission netCDF file INFO 2025-06-26 20:38:45,953 resample.py get_mission_start_end():1145 [1] navigation: 2014-10-09T18:45:42.532250112 to 2014-10-09T20:03:08.513978624 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:38:45,955 resample.py get_mission_start_end():1145 [1] hs2 : 2014-10-09T18:45:08.304594944 to 2014-10-09T20:03:08.443983360 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 20:38:45,958 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-10-09T18:45:30.433079040 to 2014-10-09T20:03:08.313992192 (0 days 00:00:00.199986432 before mission_end) INFO 2025-06-26 20:38:45,959 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-10-09T18:45:30.713059840 to 2014-10-09T20:03:08.313992192 (0 days 00:00:00.199986432 before mission_end) INFO 2025-06-26 20:38:45,960 resample.py get_mission_start_end():1145 [1] isus : 2014-10-09T18:46:15.260008192 to 2014-10-09T20:03:08.353989632 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 20:38:45,962 resample.py get_mission_start_end():1145 [1] biolume : 2014-10-09T18:44:59.295177984 to 2014-10-09T20:03:07.304027392 (0 days 00:00:01.209951232 before mission_end) INFO 2025-06-26 20:38:45,963 resample.py get_mission_start_end():1145 [1] tailcone : 2014-10-09T18:44:57.865310208 to 2014-10-09T20:03:08.423984640 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 20:38:45,963 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_align.nc mission netCDF file INFO 2025-06-26 20:38:45,964 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,058 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,077 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,099 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,121 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,144 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,166 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,188 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,209 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,230 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,249 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,269 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,288 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,308 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,328 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,343 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,356 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,370 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,385 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,400 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,420 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,440 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,463 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,485 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,508 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,527 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,543 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,559 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,574 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,587 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:46,593 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:38:46,593 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:38:46,775 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:38:46,808 resample.py add_biolume_proxies():633 [1] Zero flow values found: 4689 of 4689 - replaced with 350 ml/s INFO 2025-06-26 20:38:46,809 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:38:46,828 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:38:46,838 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:38:46,847 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:38:46,847 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:38:46,877 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:38:47,066 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_1S.nc INFO 2025-06-26 20:38:48,624 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:38:54,370 create_products.py gulper_odv():522 [1] Wrote 5 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.282.03/dorado_2014.282.03_1S_Gulper.txt INFO 2025-06-26 20:38:54,371 process.py archive():337 [1] Archiving steps for 2014.282.03 INFO 2025-06-26 20:38:54,371 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03, BASE_PATH = /data/auv_data INFO 2025-06-26 20:38:54,373 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:38:54,373 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.282.03_1S.nc INFO 2025-06-26 20:38:54,384 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:38:54,385 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.282.03_cal.nc INFO 2025-06-26 20:38:54,423 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:38:54,424 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.282.03_align.nc INFO 2025-06-26 20:38:54,474 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:38:54,488 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,500 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,504 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,514 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,541 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,553 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,563 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,581 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,588 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014282/2014.282.03 done. INFO 2025-06-26 20:38:54,588 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:38:54,589 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.282.03_1S_Gulper.txt INFO 2025-06-26 20:38:54,594 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.282.03/dorado_2014.282.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:38:54,594 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.282.03/dorado_2014.282.03_processing.log /Volumes/AUVCTD/surveys/2014/netcdf