INFO 2025-06-26 19:33:30,983 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 19:33:30,983 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Molecular Ecology - August 2013 - North Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:33:30,983 process.py process_mission():449 [1] Processing SIMZ August 2013 mission 2013.225.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:33:30,983 process.py download_process():165 [1] Download and processing steps for 2013.225.00 INFO 2025-06-26 19:33:30,983 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013225/2013.225.00 INFO 2025-06-26 19:33:30,983 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013225/2013.225.00 to /data/auv_data/dorado/missionlogs/2013.225.00 INFO 2025-06-26 19:33:33,795 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.225.00 INFO 2025-06-26 19:33:33,796 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/ctdDriver.log (3058854 bytes) INFO 2025-06-26 19:33:34,014 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/ctdDriver2.log (3059039 bytes) INFO 2025-06-26 19:33:34,227 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.225.00/ctdDriver2.log: [1] INFO 2025-06-26 19:33:34,234 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/gps.log (126716 bytes) INFO 2025-06-26 19:33:34,254 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/hydroscatlog.log (2686174 bytes) INFO 2025-06-26 19:33:34,536 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/navigation.log (10843958 bytes) INFO 2025-06-26 19:33:35,288 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/isuslog.log (236469 bytes) INFO 2025-06-26 19:33:35,315 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.225.00/isuslog.log: [3] INFO 2025-06-26 19:33:35,316 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/parosci.log (3777302 bytes) INFO 2025-06-26 19:33:35,626 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/tailCone.log (1920907 bytes) INFO 2025-06-26 19:33:35,859 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/biolume.log (2237490 bytes) INFO 2025-06-26 19:33:36,080 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:33:36,192 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.40 seconds INFO 2025-06-26 19:33:36,192 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.225.00/lopc.bin (32961715 bytes) INFO 2025-06-26 19:33:36,193 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:33:36 2025 INFO 2025-06-26 19:33:36,193 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.225.00/parosci.nc INFO 2025-06-26 19:33:36,193 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:33:36,193 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.225.00/parosci.nc INFO 2025-06-26 19:33:36,196 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1376406507.1, sensor_off_time = 1376414506.5 INFO 2025-06-26 19:33:36,196 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 7999 seconds. Expecting to read 15998 L frames from the lopc.bin file. INFO 2025-06-26 19:33:36,196 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 15998 records from the lopc.bin file. INFO 2025-06-26 19:33:36,291 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-08-13 15:08:27 Z and endTime = 2013-08-13 17:21:46 Z with 15998 records expected to be read from lopc.bin INFO 2025-06-26 19:33:36,291 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.225.00/lopc.bin INFO 2025-06-26 19:33:36,291 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.225.00/lopc.nc INFO 2025-06-26 19:33:36,291 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.225.00/lopc.nc INFO 2025-06-26 19:33:36,291 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.225.00 INFO 2025-06-26 19:33:36,292 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:33:36,336 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:33:36,336 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:33:36,336 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:33:36,524 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:33:36,525 process.py calibrate():227 [1] Calibration steps for 2013.225.00 INFO 2025-06-26 19:33:36,637 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 19:33:36,639 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:33:37,135 calibrate.py _nudge_pos():1806 [1] 83: 0.110 -0.0000636 -0.0006705 655 2.18 -4.323 -56.994 2013-08-13T15:11:51.735341568 INFO 2025-06-26 19:33:37,145 calibrate.py _nudge_pos():1806 [1] 84: 0.110 -0.0000164 -0.0000175 90 0.30 -8.187 -10.913 2013-08-13T15:12:09.734108416 INFO 2025-06-26 19:33:37,666 calibrate.py _nudge_pos():1806 [1] 141: 0.120 0.0083293 -0.0055342 8870 29.56 41.734 -34.688 2013-08-13T15:42:39.728745216 INFO 2025-06-26 19:33:38,079 calibrate.py _nudge_pos():1806 [1] 186: 0.120 0.0061753 -0.0079087 9770 32.56 28.097 -45.004 2013-08-13T16:15:57.731872512 INFO 2025-06-26 19:33:38,527 calibrate.py _nudge_pos():1806 [1] 233: 0.120 0.0034277 -0.0063958 7840 26.13 19.438 -45.355 2013-08-13T16:42:51.731305984 INFO 2025-06-26 19:33:38,987 calibrate.py _nudge_pos():1806 [1] 283: 0.120 0.0003934 -0.0029553 4105 13.68 4.261 -40.030 2013-08-13T16:57:21.731707136 INFO 2025-06-26 19:33:52,524 calibrate.py _nudge_pos():1862 [1] 1712: - - - 4 0.01 - - INFO 2025-06-26 19:33:52,524 calibrate.py _nudge_pos():1868 [1] Points in final series = 39859 INFO 2025-06-26 19:33:52,971 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:33:53,288 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:33:53,525 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:33:53,527 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.225.00/ctd1.nc INFO 2025-06-26 19:33:53,528 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 19:33:53,529 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 19:33:53,529 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:33:55,304 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:33:55,543 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 35 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:33:55,545 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.225.00/ctd2.nc INFO 2025-06-26 19:33:55,547 calibrate.py _range_qc_combined_nc():898 [1] Setting 39 ctd2_salinity values to NaN INFO 2025-06-26 19:33:55,547 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 19:33:55,547 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:33:55,904 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:33:56,238 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62] INFO 2025-06-26 19:33:56,311 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:34:03,590 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.225.00 ERROR 2025-06-26 19:34:03,590 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.225.00 INFO 2025-06-26 19:34:03,624 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_cal.nc INFO 2025-06-26 19:34:05,174 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 19:34:05,180 process.py align():251 [1] Alignment steps for 2013.225.00 INFO 2025-06-26 19:34:05,211 align.py process_cal():139 [1] Processing dorado_2013.225.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.225.00 INFO 2025-06-26 19:34:05,226 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:05,228 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:05,262 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:05,265 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:05,297 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:05,301 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:05,320 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:34:05,321 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:34:05,334 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:34:05,337 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:05,369 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,372 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,402 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,405 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,434 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,438 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,467 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,470 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,500 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,503 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,533 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,536 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,565 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,569 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,599 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,602 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,632 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,635 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,667 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,670 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,702 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,706 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,738 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,741 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,773 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,776 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,809 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,812 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,844 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,847 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,879 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,882 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,912 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,915 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,945 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,948 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:05,978 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:05,981 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:06,013 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:06,016 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:06,047 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:06,050 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:06,080 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.225.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:34:06,083 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:34:06,120 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:34:06,149 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:34:06,178 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:34:06,209 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:34:06,240 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:34:06,284 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 19:34:06,498 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:34:06,524 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_align.nc INFO 2025-06-26 19:34:06,612 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 19:34:06,615 process.py resample():273 [1] Resampling steps for 2013.225.00 INFO 2025-06-26 19:34:06,615 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:34:06,644 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_align.nc mission netCDF file INFO 2025-06-26 19:34:06,649 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_align.nc mission netCDF file INFO 2025-06-26 19:34:06,650 resample.py get_mission_start_end():1145 [1] navigation: 2013-08-13T15:08:54.957451520 to 2013-08-13T17:21:46.531361280 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 19:34:06,652 resample.py get_mission_start_end():1145 [1] hs2 : 2013-08-13T15:08:31.899031040 to 2013-08-13T17:21:46.391371008 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 19:34:06,654 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-08-13T15:09:02.616926976 to 2013-08-13T17:21:46.431368192 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 19:34:06,655 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-08-13T15:09:02.376943360 to 2013-08-13T17:21:46.391371008 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 19:34:06,656 resample.py get_mission_start_end():1145 [1] isus : 2013-08-13T15:09:21.445636864 to 2013-08-13T17:21:46.351373568 (0 days 00:00:00.249982976 before mission_end) INFO 2025-06-26 19:34:06,658 resample.py get_mission_start_end():1145 [1] biolume : 2013-08-13T15:08:25.199456000 to 2013-08-13T17:21:46.001363456 (0 days 00:00:00.599993088 before mission_end) INFO 2025-06-26 19:34:06,659 resample.py get_mission_start_end():1145 [1] tailcone : 2013-08-13T15:08:25.259485952 to 2013-08-13T17:21:46.601356544 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:34:06,660 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_align.nc mission netCDF file INFO 2025-06-26 19:34:06,660 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,763 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,783 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,802 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,822 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,840 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,857 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,875 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,892 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,908 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,924 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,940 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,955 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,971 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:06,986 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,002 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,017 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,033 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,051 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,070 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,089 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,108 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,126 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,143 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,160 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,173 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,184 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,195 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,205 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,214 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,218 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:34:07,218 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:34:07,510 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:34:07,561 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:34:07,590 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:34:07,603 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:34:07,616 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:34:07,616 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:34:07,640 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:34:07,795 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_1S.nc INFO 2025-06-26 19:34:09,445 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:34:20,290 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.225.00/dorado_2013.225.00_1S_Gulper.txt INFO 2025-06-26 19:34:20,290 process.py archive():337 [1] Archiving steps for 2013.225.00 INFO 2025-06-26 19:34:20,290 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:34:20,290 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:34:20,291 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.225.00_1S.nc INFO 2025-06-26 19:34:20,305 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:34:20,306 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.225.00_cal.nc INFO 2025-06-26 19:34:20,365 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:34:20,366 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.225.00_align.nc INFO 2025-06-26 19:34:20,449 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:34:20,465 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,477 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,482 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,494 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,529 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,542 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,553 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,577 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,582 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013225/2013.225.00 done. INFO 2025-06-26 19:34:20,582 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:34:20,584 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.225.00_1S_Gulper.txt INFO 2025-06-26 19:34:20,588 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.225.00/dorado_2013.225.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:34:20,588 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.225.00/dorado_2013.225.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf