INFO 2025-06-26 20:00:40,908 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 20:00:40,908 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Autonomy group's short missions in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:00:40,908 process.py process_mission():449 [1] Processing AUVCTD mission 2013.287.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:00:40,908 process.py download_process():165 [1] Download and processing steps for 2013.287.01 INFO 2025-06-26 20:00:40,908 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013287/2013.287.01 INFO 2025-06-26 20:00:40,908 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013287/2013.287.01 to /data/auv_data/dorado/missionlogs/2013.287.01 INFO 2025-06-26 20:00:42,032 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.287.01 INFO 2025-06-26 20:00:42,032 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/ctdDriver.log (1437894 bytes) INFO 2025-06-26 20:00:42,145 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/ctdDriver2.log (1437791 bytes) INFO 2025-06-26 20:00:42,251 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/gps.log (204332 bytes) INFO 2025-06-26 20:00:42,281 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/hydroscatlog.log (1262458 bytes) INFO 2025-06-26 20:00:42,416 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/navigation.log (5072390 bytes) INFO 2025-06-26 20:00:42,789 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/parosci.log (1776182 bytes) INFO 2025-06-26 20:00:42,942 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/tailCone.log (903019 bytes) INFO 2025-06-26 20:00:43,064 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/biolume.log (1054062 bytes) INFO 2025-06-26 20:00:43,174 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:00:43,231 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.20 seconds INFO 2025-06-26 20:00:43,231 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.01/lopc.bin (4339326 bytes) INFO 2025-06-26 20:00:43,231 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:00:43 2025 INFO 2025-06-26 20:00:43,231 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.287.01/parosci.nc INFO 2025-06-26 20:00:43,231 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:00:43,231 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.287.01/parosci.nc INFO 2025-06-26 20:00:43,233 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381768749.0, sensor_off_time = 1381772509.7 INFO 2025-06-26 20:00:43,234 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 3760 seconds. Expecting to read 7520 L frames from the lopc.bin file. INFO 2025-06-26 20:00:43,234 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 7520 records from the lopc.bin file. INFO 2025-06-26 20:00:43,279 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-14 16:39:08 Z and endTime = 2013-10-14 17:41:49 Z with 7520 records expected to be read from lopc.bin INFO 2025-06-26 20:00:43,279 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.287.01/lopc.bin INFO 2025-06-26 20:00:43,279 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.287.01/lopc.nc INFO 2025-06-26 20:00:43,279 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.287.01/lopc.nc INFO 2025-06-26 20:00:43,280 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.287.01 INFO 2025-06-26 20:00:43,280 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:00:43,283 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:00:43,333 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:00:43,333 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:00:43,333 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:00:44,029 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:00:44,030 process.py calibrate():227 [1] Calibration steps for 2013.287.01 INFO 2025-06-26 20:00:44,117 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 20:00:44,118 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:00:49,619 calibrate.py _nudge_pos():1806 [1] 626: 0.040 -0.0015009 -0.0010279 3795 12.65 -17.585 -15.060 2013-10-14T17:02:10.119423744 INFO 2025-06-26 20:00:50,739 calibrate.py _nudge_pos():1806 [1] 746: 0.040 -0.0002411 -0.0002255 845 2.81 -12.700 -14.851 2013-10-14T17:06:58.119694336 INFO 2025-06-26 20:00:50,803 calibrate.py _nudge_pos():1806 [1] 753: 0.040 -0.0000045 -0.0000135 65 0.21 -3.155 -11.758 2013-10-14T17:07:17.118392832 INFO 2025-06-26 20:01:09,934 calibrate.py _nudge_pos():1862 [1] 2791: - - - 3 0.01 - - INFO 2025-06-26 20:01:09,934 calibrate.py _nudge_pos():1868 [1] Points in final series = 18640 INFO 2025-06-26 20:01:10,119 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:01:10,278 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:01:10,392 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:01:10,393 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.287.01/ctd1.nc INFO 2025-06-26 20:01:10,394 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:01:10,395 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 20:01:10,395 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:01:10,540 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:01:10,654 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:01:10,656 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.287.01/ctd2.nc INFO 2025-06-26 20:01:10,657 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:01:10,657 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 20:01:10,657 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:01:10,658 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.287.01 INFO 2025-06-26 20:01:10,661 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:01:10,892 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 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90] INFO 2025-06-26 20:01:10,927 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:01:14,317 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.287.01 ERROR 2025-06-26 20:01:14,317 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.287.01 INFO 2025-06-26 20:01:14,335 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_cal.nc INFO 2025-06-26 20:01:14,395 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, 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 20:01:14,401 process.py align():251 [1] Alignment steps for 2013.287.01 INFO 2025-06-26 20:01:14,427 align.py process_cal():139 [1] Processing dorado_2013.287.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.287.01 INFO 2025-06-26 20:01:14,436 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:01:14,438 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:01:14,458 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:01:14,461 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:01:14,480 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:01:14,482 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:01:14,494 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:01:14,494 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:01:14,502 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:01:14,504 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:01:14,522 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,524 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,543 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,545 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,563 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,565 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,583 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,585 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,603 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,605 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,623 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,625 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,643 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,645 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,663 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,666 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,683 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,685 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,703 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,705 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,724 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,726 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,744 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,746 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,764 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,767 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,785 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,787 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,806 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,808 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,827 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,829 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,848 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,851 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,869 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,872 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,891 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,894 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,912 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,915 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,933 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,936 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,955 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:01:14,957 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:01:14,981 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:01:15,002 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:01:15,027 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:01:15,138 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:01:15,155 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_align.nc INFO 2025-06-26 20:01:15,217 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, 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 20:01:15,219 process.py resample():273 [1] Resampling steps for 2013.287.01 INFO 2025-06-26 20:01:15,220 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:01:15,244 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_align.nc mission netCDF file INFO 2025-06-26 20:01:15,248 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_align.nc mission netCDF file INFO 2025-06-26 20:01:15,249 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-14T16:39:41.921781504 to 2013-10-14T17:41:49.716410112 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:01:15,250 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-14T16:39:13.613720576 to 2013-10-14T17:41:49.466427136 (0 days 00:00:00.249982976 before mission_end) INFO 2025-06-26 20:01:15,252 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-14T16:39:27.062799360 to 2013-10-14T17:41:49.466427136 (0 days 00:00:00.249982976 before mission_end) INFO 2025-06-26 20:01:15,253 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-14T16:39:27.412775424 to 2013-10-14T17:41:49.566420224 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:01:15,254 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-14T16:39:06.604166656 to 2013-10-14T17:41:48.986425856 (0 days 00:00:00.729984256 before mission_end) INFO 2025-06-26 20:01:15,255 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-14T16:39:09.454005760 to 2013-10-14T17:41:49.626416128 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 20:01:15,256 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_align.nc mission netCDF file INFO 2025-06-26 20:01:15,256 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,319 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,332 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,345 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,357 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,370 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,382 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,394 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,405 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,416 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,426 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,437 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,447 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,459 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,470 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,481 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,492 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,503 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,515 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,527 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,539 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,551 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,563 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,575 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,588 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,596 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,603 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,606 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:01:15,606 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:01:15,747 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:01:15,772 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:01:15,787 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:01:15,794 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:01:15,801 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:01:15,801 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:01:15,818 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:01:15,940 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_1S.nc INFO 2025-06-26 20:01:17,189 create_products.py gulper_odv():401 [1] No gulper times found for 2013.287.01 INFO 2025-06-26 20:01:17,189 process.py archive():337 [1] Archiving steps for 2013.287.01 INFO 2025-06-26 20:01:17,189 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:01:17,190 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:01:17,192 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.01_1S.nc INFO 2025-06-26 20:01:17,203 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:01:17,204 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.01_cal.nc INFO 2025-06-26 20:01:17,235 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:01:17,236 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.01_align.nc INFO 2025-06-26 20:01:17,278 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:01:17,289 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,298 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,303 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,311 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,329 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,339 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,347 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,362 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,369 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.01 done. INFO 2025-06-26 20:01:17,369 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:01:17,369 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.01/dorado_2013.287.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf