INFO 2025-06-26 20:20:06,676 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 20:20:06,677 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:20:06,677 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.107.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:20:06,677 process.py download_process():165 [1] Download and processing steps for 2014.107.00 INFO 2025-06-26 20:20:06,677 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014107/2014.107.00 INFO 2025-06-26 20:20:06,677 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014107/2014.107.00 to /data/auv_data/dorado/missionlogs/2014.107.00 INFO 2025-06-26 20:20:10,012 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.107.00 INFO 2025-06-26 20:20:10,013 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/ctdDriver.log (4231110 bytes) INFO 2025-06-26 20:20:10,304 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/ctdDriver2.log (4237535 bytes) INFO 2025-06-26 20:20:10,606 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/gps.log (38444 bytes) INFO 2025-06-26 20:20:10,618 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/hydroscatlog.log (3713746 bytes) INFO 2025-06-26 20:20:10,989 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.107.00/hydroscatlog.log: [17893] INFO 2025-06-26 20:20:10,998 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/navigation.log (15862338 bytes) INFO 2025-06-26 20:20:12,140 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/isuslog.log (274357 bytes) INFO 2025-06-26 20:20:12,170 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/parosci.log (5212694 bytes) INFO 2025-06-26 20:20:12,601 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/tailCone.log (2654779 bytes) INFO 2025-06-26 20:20:12,931 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/biolume.log (3091762 bytes) INFO 2025-06-26 20:20:13,235 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:20:13,390 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.38 seconds INFO 2025-06-26 20:20:13,391 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.107.00/lopc.bin (33629359 bytes) INFO 2025-06-26 20:20:13,391 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:20:13 2025 INFO 2025-06-26 20:20:13,391 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.107.00/parosci.nc INFO 2025-06-26 20:20:13,391 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:20:13,391 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.107.00/parosci.nc INFO 2025-06-26 20:20:13,394 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397745799.3, sensor_off_time = 1397756858.4 INFO 2025-06-26 20:20:13,394 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11059 seconds. Expecting to read 22118 L frames from the lopc.bin file. INFO 2025-06-26 20:20:13,394 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22118 records from the lopc.bin file. INFO 2025-06-26 20:20:13,525 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-17 14:43:19 Z and endTime = 2014-04-17 17:47:38 Z with 22118 records expected to be read from lopc.bin INFO 2025-06-26 20:20:13,525 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.107.00/lopc.bin INFO 2025-06-26 20:20:13,525 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.107.00/lopc.nc INFO 2025-06-26 20:20:13,525 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.107.00/lopc.nc INFO 2025-06-26 20:20:13,526 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.107.00 INFO 2025-06-26 20:20:13,526 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:20:13,695 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:20:13,695 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:20:13,695 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:20:13,793 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:20:13,794 process.py calibrate():227 [1] Calibration steps for 2014.107.00 INFO 2025-06-26 20:20:13,926 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 20:20:13,928 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:20:14,642 calibrate.py _nudge_pos():1806 [1] 113: 0.120 -0.0003263 0.0001136 720 2.40 -21.006 8.785 2014-04-17T14:47:33.872214272 INFO 2025-06-26 20:20:15,161 calibrate.py _nudge_pos():1806 [1] 169: 0.130 0.0008158 -0.0003153 8065 26.88 4.684 -2.174 2014-04-17T15:15:21.867948800 INFO 2025-06-26 20:20:15,717 calibrate.py _nudge_pos():1806 [1] 229: 0.120 0.0006032 -0.0005091 10345 34.48 2.701 -2.736 2014-04-17T15:50:49.872170496 INFO 2025-06-26 20:20:16,275 calibrate.py _nudge_pos():1806 [1] 288: 0.130 -0.0005153 -0.0002014 8270 27.56 -2.887 -1.354 2014-04-17T16:19:21.874890240 INFO 2025-06-26 20:20:16,811 calibrate.py _nudge_pos():1806 [1] 345: 0.140 -0.0028500 0.0003318 8880 29.60 -14.871 2.077 2014-04-17T16:49:53.869390080 INFO 2025-06-26 20:20:17,314 calibrate.py _nudge_pos():1806 [1] 399: 0.130 -0.0023686 -0.0000727 7500 25.00 -14.636 -0.539 2014-04-17T17:15:46.873001984 INFO 2025-06-26 20:20:17,798 calibrate.py _nudge_pos():1806 [1] 451: 0.140 -0.0022882 0.0007040 8950 29.83 -11.850 4.373 2014-04-17T17:46:27.866885376 INFO 2025-06-26 20:20:18,463 calibrate.py _nudge_pos():1862 [1] 476: - - - 2 0.00 - - INFO 2025-06-26 20:20:18,463 calibrate.py _nudge_pos():1868 [1] Points in final series = 55069 INFO 2025-06-26 20:20:24,393 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:20:24,825 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:20:25,172 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:20:25,174 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.107.00/ctd1.nc INFO 2025-06-26 20:20:25,175 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:20:25,176 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 20:20:25,176 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:20:25,578 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:20:25,923 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:20:25,925 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.107.00/ctd2.nc INFO 2025-06-26 20:20:25,926 calibrate.py _range_qc_combined_nc():898 [1] Setting 34 ctd2_salinity values to NaN INFO 2025-06-26 20:20:25,926 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 20:20:25,926 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:20:25,948 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:20:26,483 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65] INFO 2025-06-26 20:20:26,580 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 20:20:36,658 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.107.00 ERROR 2025-06-26 20:20:36,658 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.107.00 INFO 2025-06-26 20:20:36,703 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_cal.nc INFO 2025-06-26 20:20:36,802 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:20:36,807 process.py align():251 [1] Alignment steps for 2014.107.00 INFO 2025-06-26 20:20:36,839 align.py process_cal():139 [1] Processing dorado_2014.107.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.107.00 INFO 2025-06-26 20:20:36,858 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:20:36,861 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:20:36,902 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:20:36,905 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:20:36,955 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:20:36,959 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:20:36,983 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:20:36,983 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:20:36,999 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:20:37,002 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:20:37,044 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,047 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,084 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,087 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,124 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,127 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,163 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,166 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,203 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,206 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,243 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,246 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,283 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,286 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,322 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,325 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,361 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,364 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,400 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,404 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,440 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,444 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,479 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,482 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,519 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,522 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,558 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,560 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,598 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,601 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,637 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,640 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,678 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,681 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,718 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,721 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,758 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,761 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,798 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,801 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,838 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,841 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,878 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.107.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:20:37,881 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:20:37,927 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:20:37,961 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:20:37,995 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:20:38,032 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:20:38,068 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:20:38,123 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:20:38,406 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:20:38,437 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_align.nc INFO 2025-06-26 20:20:38,539 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:20:38,541 process.py resample():273 [1] Resampling steps for 2014.107.00 INFO 2025-06-26 20:20:38,542 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:20:38,572 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_align.nc mission netCDF file INFO 2025-06-26 20:20:38,577 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_align.nc mission netCDF file INFO 2025-06-26 20:20:38,579 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-17T14:44:04.686544640 to 2014-04-17T17:47:38.272062208 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:20:38,580 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-17T14:43:24.269313280 to 2014-04-17T17:47:38.322059008 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 20:20:38,582 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-17T14:44:02.076723456 to 2014-04-17T17:47:38.332058112 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:20:38,583 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-17T14:43:45.387866624 to 2014-04-17T17:47:38.392054016 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:20:38,585 resample.py get_mission_start_end():1145 [1] isus : 2014-04-17T14:44:33.434575104 to 2014-04-17T17:47:38.192067584 (0 days 00:00:00.199986432 before mission_end) INFO 2025-06-26 20:20:38,586 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-17T14:43:17.889716224 to 2014-04-17T17:47:37.872055296 (0 days 00:00:00.519998720 before mission_end) INFO 2025-06-26 20:20:38,587 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-17T14:43:19.229658624 to 2014-04-17T17:47:38.352056832 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 20:20:38,588 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_align.nc mission netCDF file INFO 2025-06-26 20:20:38,589 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,721 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,746 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,770 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,793 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,815 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,836 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,856 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,877 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,896 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,916 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,935 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,954 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,975 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:38,995 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,015 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,034 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,054 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,076 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,098 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,120 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,141 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,161 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,182 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,203 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,216 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,228 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,240 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,250 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,260 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:39,264 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:20:39,264 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:20:39,653 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:20:39,722 resample.py add_biolume_proxies():633 [1] Zero flow values found: 11061 of 11061 - replaced with 350 ml/s INFO 2025-06-26 20:20:39,722 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:20:39,761 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:20:39,779 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:20:39,795 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:20:39,795 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:20:39,823 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:20:40,001 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_1S.nc INFO 2025-06-26 20:20:42,096 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:20:53,234 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.107.00/dorado_2014.107.00_1S_Gulper.txt INFO 2025-06-26 20:20:53,235 process.py archive():337 [1] Archiving steps for 2014.107.00 INFO 2025-06-26 20:20:53,235 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:20:53,235 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:20:53,236 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.107.00_1S.nc INFO 2025-06-26 20:20:53,250 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:20:53,250 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.107.00_cal.nc INFO 2025-06-26 20:20:53,324 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:20:53,325 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.107.00_align.nc INFO 2025-06-26 20:20:53,436 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:20:53,453 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,468 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,472 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,486 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,527 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,532 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,549 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,562 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,594 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,599 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014107/2014.107.00 done. INFO 2025-06-26 20:20:53,599 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:20:53,600 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.107.00_1S_Gulper.txt INFO 2025-06-26 20:20:53,605 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.107.00/dorado_2014.107.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:20:53,606 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.107.00/dorado_2014.107.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf