INFO 2025-06-26 20:22:13,703 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 20:22:13,703 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:22:13,703 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.109.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:22:13,703 process.py download_process():165 [1] Download and processing steps for 2014.109.00 INFO 2025-06-26 20:22:13,703 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014109/2014.109.00 INFO 2025-06-26 20:22:13,704 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014109/2014.109.00 to /data/auv_data/dorado/missionlogs/2014.109.00 INFO 2025-06-26 20:22:16,865 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.109.00 INFO 2025-06-26 20:22:16,865 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/ctdDriver.log (4117446 bytes) INFO 2025-06-26 20:22:17,159 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/ctdDriver2.log (4123295 bytes) INFO 2025-06-26 20:22:17,456 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/gps.log (32900 bytes) INFO 2025-06-26 20:22:17,467 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/hydroscatlog.log (3613534 bytes) INFO 2025-06-26 20:22:17,838 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/navigation.log (15435522 bytes) INFO 2025-06-26 20:22:18,930 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/isuslog.log (266677 bytes) INFO 2025-06-26 20:22:18,960 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/parosci.log (5073110 bytes) INFO 2025-06-26 20:22:19,384 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/tailCone.log (2583499 bytes) INFO 2025-06-26 20:22:19,708 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/biolume.log (3009118 bytes) INFO 2025-06-26 20:22:20,001 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:22:20,153 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.29 seconds INFO 2025-06-26 20:22:20,154 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.00/lopc.bin (32138161 bytes) INFO 2025-06-26 20:22:20,154 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:22:20 2025 INFO 2025-06-26 20:22:20,154 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.109.00/parosci.nc INFO 2025-06-26 20:22:20,154 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:22:20,154 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.109.00/parosci.nc INFO 2025-06-26 20:22:20,158 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397919322.0, sensor_off_time = 1397930084.2 INFO 2025-06-26 20:22:20,158 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10762 seconds. Expecting to read 21524 L frames from the lopc.bin file. INFO 2025-06-26 20:22:20,158 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21524 records from the lopc.bin file. INFO 2025-06-26 20:22:20,285 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-19 14:55:21 Z and endTime = 2014-04-19 17:54:44 Z with 21524 records expected to be read from lopc.bin INFO 2025-06-26 20:22:20,285 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.109.00/lopc.bin INFO 2025-06-26 20:22:20,285 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.109.00/lopc.nc INFO 2025-06-26 20:22:20,285 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.109.00/lopc.nc INFO 2025-06-26 20:22:20,286 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.109.00 INFO 2025-06-26 20:22:20,286 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:22:20,326 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:22:20,326 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:22:20,326 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:22:29,436 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:22:29,437 process.py calibrate():227 [1] Calibration steps for 2014.109.00 INFO 2025-06-26 20:22:29,569 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 20:22:29,571 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:22:30,200 calibrate.py _nudge_pos():1806 [1] 106: 0.130 -0.0007057 0.0001625 2490 8.30 -13.141 3.630 2014-04-19T15:05:21.930132992 INFO 2025-06-26 20:22:30,731 calibrate.py _nudge_pos():1806 [1] 164: 0.130 -0.0049939 0.0018444 10005 33.35 -23.129 10.249 2014-04-19T15:39:39.929150464 INFO 2025-06-26 20:22:31,271 calibrate.py _nudge_pos():1806 [1] 223: 0.140 -0.0051908 0.0022642 9940 33.13 -24.191 12.664 2014-04-19T16:13:45.928990208 INFO 2025-06-26 20:22:31,639 calibrate.py _nudge_pos():1806 [1] 263: 0.130 -0.0042869 0.0021682 10095 33.65 -19.667 11.941 2014-04-19T16:48:03.938006528 INFO 2025-06-26 20:22:32,166 calibrate.py _nudge_pos():1806 [1] 320: 0.140 -0.0035011 0.0014396 9470 31.56 -17.118 8.452 2014-04-19T17:20:33.934422784 INFO 2025-06-26 20:22:32,639 calibrate.py _nudge_pos():1806 [1] 371: 0.150 -0.0028316 0.0013541 8030 26.76 -16.325 9.375 2014-04-19T17:48:09.930979328 INFO 2025-06-26 20:22:33,168 calibrate.py _nudge_pos():1806 [1] 428: 0.140 0.0000711 0.0005611 1610 5.36 2.045 19.385 2014-04-19T17:54:27.935084288 INFO 2025-06-26 20:22:33,322 calibrate.py _nudge_pos():1862 [1] 397: - - - 1 0.00 - - INFO 2025-06-26 20:22:33,322 calibrate.py _nudge_pos():1868 [1] Points in final series = 53586 INFO 2025-06-26 20:22:33,815 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:22:34,225 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:22:34,553 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:22:34,555 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.109.00/ctd1.nc INFO 2025-06-26 20:22:34,556 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:22:34,556 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 20:22:34,556 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:22:34,941 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:22:35,262 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:22:35,264 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.109.00/ctd2.nc INFO 2025-06-26 20:22:35,266 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:22:35,266 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 20:22:35,266 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:22:35,287 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:22:35,828 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:22:35,850 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.109.00 ERROR 2025-06-26 20:22:35,850 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.109.00 INFO 2025-06-26 20:22:35,895 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_cal.nc INFO 2025-06-26 20:22:35,992 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 20:22:35,998 process.py align():251 [1] Alignment steps for 2014.109.00 INFO 2025-06-26 20:22:36,030 align.py process_cal():139 [1] Processing dorado_2014.109.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.109.00 INFO 2025-06-26 20:22:36,049 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:22:36,052 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:22:36,094 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:22:36,097 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:22:36,138 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:22:36,141 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:22:36,165 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:22:36,165 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:22:36,180 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:22:36,183 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:22:36,223 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,226 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,261 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,264 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,300 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,303 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,338 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,341 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,377 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,380 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,414 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,418 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,453 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,456 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,493 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,568 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,606 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,609 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,644 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,647 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,683 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,686 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,721 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,724 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,760 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,763 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,800 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,803 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,839 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,843 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,881 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,884 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,921 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,924 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:36,960 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:36,964 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:37,002 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:37,005 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:37,042 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:37,045 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:37,082 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:37,085 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:37,122 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:22:37,125 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:22:37,170 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:22:37,203 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:22:37,236 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:22:37,270 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:22:37,306 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:22:37,365 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:22:37,646 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:22:37,676 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_align.nc INFO 2025-06-26 20:22:37,776 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 20:22:37,779 process.py resample():273 [1] Resampling steps for 2014.109.00 INFO 2025-06-26 20:22:37,779 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:22:37,809 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_align.nc mission netCDF file INFO 2025-06-26 20:22:37,815 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_align.nc mission netCDF file INFO 2025-06-26 20:22:37,816 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-19T14:56:06.948152064 to 2014-04-19T17:54:44.143973888 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 20:22:37,818 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-19T14:55:27.840830976 to 2014-04-19T17:54:44.163972608 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:22:37,819 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-19T14:56:03.778369280 to 2014-04-19T17:54:44.033981440 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 20:22:37,820 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-19T14:55:47.149508352 to 2014-04-19T17:54:44.153972992 (0 days 00:00:00.009999616 before mission_end) INFO 2025-06-26 20:22:37,822 resample.py get_mission_start_end():1145 [1] isus : 2014-04-19T14:56:35.166219008 to 2014-04-19T17:54:44.063979264 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 20:22:37,823 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-19T14:55:19.631359232 to 2014-04-19T17:54:43.413989632 (0 days 00:00:00.749982976 before mission_end) INFO 2025-06-26 20:22:37,825 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-19T14:55:21.931236096 to 2014-04-19T17:54:44.143973888 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 20:22:37,825 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_align.nc mission netCDF file INFO 2025-06-26 20:22:37,826 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:37,955 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:37,978 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,001 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,025 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,046 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,067 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,087 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,108 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,126 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,145 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,163 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,182 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,200 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,218 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,237 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,255 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,273 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,293 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,314 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,334 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,353 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,374 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,396 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,417 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,430 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,441 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,452 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,463 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,473 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:38,477 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:22:38,477 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:22:38,849 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:22:38,918 resample.py add_biolume_proxies():633 [1] Zero flow values found: 10765 of 10765 - replaced with 350 ml/s INFO 2025-06-26 20:22:38,919 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:22:38,958 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:22:38,975 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:22:38,990 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:22:38,990 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:22:39,020 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:39,191 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_1S.nc INFO 2025-06-26 20:22:40,878 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:22:51,686 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.109.00/dorado_2014.109.00_1S_Gulper.txt INFO 2025-06-26 20:22:51,686 process.py archive():337 [1] Archiving steps for 2014.109.00 INFO 2025-06-26 20:22:51,686 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:22:51,687 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:22:51,688 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.109.00_1S.nc INFO 2025-06-26 20:22:51,703 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:22:51,703 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.109.00_cal.nc INFO 2025-06-26 20:22:51,784 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:22:51,785 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.109.00_align.nc INFO 2025-06-26 20:22:51,892 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:22:51,908 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:51,923 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:51,928 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:51,942 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:51,986 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:51,992 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:52,008 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:52,023 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:52,055 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:52,075 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.00 done. INFO 2025-06-26 20:22:52,075 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:22:52,077 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.109.00_1S_Gulper.txt INFO 2025-06-26 20:22:52,082 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.109.00/dorado_2014.109.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:22:52,082 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.00/dorado_2014.109.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf