INFO 2025-06-26 19:29:48,063 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 19:29:48,063 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - Outbound mission, 7 Gulpers fired - ctdToUse = ctd1 INFO 2025-06-26 19:29:48,063 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.079.04 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:29:48,063 process.py download_process():165 [1] Download and processing steps for 2013.079.04 INFO 2025-06-26 19:29:48,063 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013079/2013.079.04 INFO 2025-06-26 19:29:48,063 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013079/2013.079.04 to /data/auv_data/dorado/missionlogs/2013.079.04 INFO 2025-06-26 19:29:50,607 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.079.04 INFO 2025-06-26 19:29:50,607 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/ctdDriver.log (4113606 bytes) INFO 2025-06-26 19:29:50,901 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/ctdDriver2.log (4113695 bytes) INFO 2025-06-26 19:29:51,195 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/gps.log (60764 bytes) INFO 2025-06-26 19:29:51,210 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/hydroscatlog.log (3602782 bytes) INFO 2025-06-26 19:29:51,584 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/navigation.log (14543974 bytes) INFO 2025-06-26 19:29:52,638 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/isuslog.log (318101 bytes) INFO 2025-06-26 19:29:52,672 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.079.04/isuslog.log: [ 1 2 3 4 5 6 7 8 9 10] INFO 2025-06-26 19:29:52,673 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/parosci.log (5053766 bytes) INFO 2025-06-26 19:29:53,119 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/tailCone.log (2575579 bytes) INFO 2025-06-26 19:29:53,437 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/biolume.log (2999462 bytes) INFO 2025-06-26 19:29:53,730 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:29:53,884 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.28 seconds INFO 2025-06-26 19:29:53,884 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.079.04/lopc.bin (28661694 bytes) INFO 2025-06-26 19:29:53,885 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:29:53 2025 INFO 2025-06-26 19:29:53,885 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.079.04/parosci.nc INFO 2025-06-26 19:29:53,885 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:29:53,885 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.079.04/parosci.nc INFO 2025-06-26 19:29:53,888 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363804766.0, sensor_off_time = 1363815495.5 INFO 2025-06-26 19:29:53,888 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10729 seconds. Expecting to read 21458 L frames from the lopc.bin file. INFO 2025-06-26 19:29:53,888 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21458 records from the lopc.bin file. INFO 2025-06-26 19:29:54,015 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-20 18:39:25 Z and endTime = 2013-03-20 21:38:15 Z with 21458 records expected to be read from lopc.bin INFO 2025-06-26 19:29:54,015 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.079.04/lopc.bin INFO 2025-06-26 19:29:54,015 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.079.04/lopc.nc INFO 2025-06-26 19:29:54,016 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.079.04/lopc.nc INFO 2025-06-26 19:29:54,016 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.079.04 INFO 2025-06-26 19:29:54,016 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:29:54,019 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A015920 WARNING 2025-06-26 19:29:54,019 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:29:54,062 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:29:54,062 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:29:54,062 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:29:54,098 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:29:54,099 process.py calibrate():227 [1] Calibration steps for 2013.079.04 INFO 2025-06-26 19:29:54,232 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 19:29:54,234 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:29:55,001 calibrate.py _nudge_pos():1806 [1] 113: 0.010 0.0000665 -0.0002151 685 2.28 4.503 -17.486 2013-03-20T18:43:33.887503104 INFO 2025-06-26 19:29:55,549 calibrate.py _nudge_pos():1806 [1] 172: 0.010 0.0054431 -0.0020345 7060 23.53 35.701 -16.022 2013-03-20T19:08:03.886801152 INFO 2025-06-26 19:29:56,275 calibrate.py _nudge_pos():1806 [1] 250: 0.020 0.0076127 -0.0048041 10265 34.21 34.350 -26.019 2013-03-20T19:43:33.890885888 INFO 2025-06-26 19:29:56,861 calibrate.py _nudge_pos():1806 [1] 313: 0.030 0.0053512 -0.0053374 8270 27.56 29.977 -35.882 2013-03-20T20:12:09.883332608 INFO 2025-06-26 19:29:57,457 calibrate.py _nudge_pos():1806 [1] 374: 0.020 0.0036533 -0.0044403 7800 26.00 21.703 -31.650 2013-03-20T20:39:09.882354944 INFO 2025-06-26 19:29:58,094 calibrate.py _nudge_pos():1806 [1] 441: 0.030 0.0052154 -0.0041169 7530 25.10 32.100 -30.397 2013-03-20T21:05:21.884665344 INFO 2025-06-26 19:29:58,726 calibrate.py _nudge_pos():1806 [1] 508: 0.030 0.0057094 -0.0044030 7920 26.40 33.416 -30.908 2013-03-20T21:32:51.891632128 INFO 2025-06-26 19:30:01,771 calibrate.py _nudge_pos():1862 [1] 794: - - - 2 0.00 - - INFO 2025-06-26 19:30:01,772 calibrate.py _nudge_pos():1868 [1] Points in final series = 53462 INFO 2025-06-26 19:30:02,262 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:30:02,675 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:30:02,993 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:30:02,995 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.079.04/ctd1.nc INFO 2025-06-26 19:30:02,996 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 19:30:02,996 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 19:30:02,996 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:30:03,382 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:30:03,701 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:30:03,702 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.079.04/ctd2.nc INFO 2025-06-26 19:30:03,704 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:30:03,704 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 19:30:03,704 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:30:04,181 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:30:04,723 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 19:30:04,818 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:30:14,531 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.079.04 ERROR 2025-06-26 19:30:14,531 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.079.04 INFO 2025-06-26 19:30:14,575 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_cal.nc INFO 2025-06-26 19:30:14,672 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 19:30:14,678 process.py align():251 [1] Alignment steps for 2013.079.04 INFO 2025-06-26 19:30:14,711 align.py process_cal():139 [1] Processing dorado_2013.079.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.079.04 INFO 2025-06-26 19:30:14,729 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:30:14,732 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:30:14,773 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:30:14,776 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:30:14,818 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:30:14,822 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:30:14,845 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:30:14,845 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:30:14,861 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:30:14,864 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:30:14,905 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:14,908 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:14,946 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:14,949 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,004 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,008 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,044 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,048 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,085 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,089 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,125 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,128 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,165 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,169 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,205 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,208 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,245 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,248 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,286 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,290 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,327 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,331 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,366 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,370 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,407 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,410 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,446 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,449 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,486 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,490 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,526 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,529 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,567 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,570 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,607 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,610 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,648 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,652 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,688 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,692 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,730 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,733 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,769 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.079.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:30:15,772 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:30:15,819 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:30:15,854 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:30:15,889 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:30:15,925 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:30:15,963 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:30:16,017 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:30:16,298 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:30:16,329 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_align.nc INFO 2025-06-26 19:30:16,429 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 19:30:16,432 process.py resample():273 [1] Resampling steps for 2013.079.04 INFO 2025-06-26 19:30:16,432 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:30:16,462 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_align.nc mission netCDF file INFO 2025-06-26 19:30:16,467 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_align.nc mission netCDF file INFO 2025-06-26 19:30:16,469 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-20T18:40:03.221934592 to 2013-03-20T21:38:15.289477888 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 19:30:16,470 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-20T18:39:30.644166400 to 2013-03-20T21:38:15.209483264 (0 days 00:00:00.239983616 before mission_end) INFO 2025-06-26 19:30:16,471 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-20T18:39:45.193169664 to 2013-03-20T21:38:15.449466880 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:30:16,473 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-20T18:39:44.913188864 to 2013-03-20T21:38:15.409469696 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 19:30:16,474 resample.py get_mission_start_end():1145 [1] isus : 2013-03-20T18:40:31.469999616 to 2013-03-20T21:38:14.839508736 (0 days 00:00:00.609958144 before mission_end) INFO 2025-06-26 19:30:16,476 resample.py get_mission_start_end():1145 [1] biolume : 2013-03-20T18:39:24.434557440 to 2013-03-20T21:38:14.759480064 (0 days 00:00:00.689986816 before mission_end) INFO 2025-06-26 19:30:16,477 resample.py get_mission_start_end():1145 [1] tailcone : 2013-03-20T18:39:26.024482816 to 2013-03-20T21:38:15.429468160 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 19:30:16,478 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_align.nc mission netCDF file INFO 2025-06-26 19:30:16,478 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,607 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,631 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,655 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,679 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,700 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,721 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,742 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,762 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,781 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,800 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,819 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,838 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,857 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,876 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,895 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,914 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,933 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,955 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,975 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:16,996 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,017 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,037 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,058 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,078 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,090 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,102 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,114 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,124 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,133 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,137 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:30:17,137 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:30:17,492 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:30:17,559 resample.py add_biolume_proxies():633 [1] Zero flow values found: 4 of 10731 - replaced with 350 ml/s INFO 2025-06-26 19:30:17,560 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:30:17,597 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:30:17,614 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:30:17,628 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:30:17,629 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:30:17,656 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:30:17,829 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_1S.nc INFO 2025-06-26 19:30:21,383 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:30:30,787 create_products.py gulper_odv():522 [1] Wrote 7 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.079.04/dorado_2013.079.04_1S_Gulper.txt INFO 2025-06-26 19:30:30,787 process.py archive():337 [1] Archiving steps for 2013.079.04 INFO 2025-06-26 19:30:30,787 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04, BASE_PATH = /data/auv_data INFO 2025-06-26 19:30:30,787 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:30:30,788 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.079.04_1S.nc INFO 2025-06-26 19:30:30,802 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:30:30,803 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.079.04_cal.nc INFO 2025-06-26 19:30:30,879 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:30:30,880 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.079.04_align.nc INFO 2025-06-26 19:30:30,998 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:30:31,017 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,036 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,042 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,057 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,106 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,112 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,136 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,150 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,190 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,196 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013079/2013.079.04 done. INFO 2025-06-26 19:30:31,196 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:30:31,197 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.079.04_1S_Gulper.txt INFO 2025-06-26 19:30:31,202 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.079.04/dorado_2013.079.04_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:30:31,202 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.079.04/dorado_2013.079.04_processing.log /Volumes/AUVCTD/surveys/2013/netcdf