INFO 2025-06-26 20:22:52,110 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 20:22:52,110 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:22:52,110 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.109.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:22:52,110 process.py download_process():165 [1] Download and processing steps for 2014.109.01 INFO 2025-06-26 20:22:52,111 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014109/2014.109.01 INFO 2025-06-26 20:22:52,111 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014109/2014.109.01 to /data/auv_data/dorado/missionlogs/2014.109.01 INFO 2025-06-26 20:22:55,727 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.109.01 INFO 2025-06-26 20:22:55,727 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/ctdDriver.log (4253766 bytes) INFO 2025-06-26 20:22:56,046 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/ctdDriver2.log (4253855 bytes) INFO 2025-06-26 20:22:56,359 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/gps.log (35924 bytes) INFO 2025-06-26 20:22:56,371 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/hydroscatlog.log (3728446 bytes) INFO 2025-06-26 20:22:56,758 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/navigation.log (15936642 bytes) INFO 2025-06-26 20:22:57,880 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/isuslog.log (275253 bytes) INFO 2025-06-26 20:22:57,911 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/parosci.log (5233574 bytes) INFO 2025-06-26 20:22:58,358 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/tailCone.log (2666203 bytes) INFO 2025-06-26 20:22:58,684 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/biolume.log (3104258 bytes) INFO 2025-06-26 20:22:58,982 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:22:59,137 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.41 seconds INFO 2025-06-26 20:22:59,137 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.109.01/lopc.bin (31450648 bytes) INFO 2025-06-26 20:22:59,138 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:22:59 2025 INFO 2025-06-26 20:22:59,138 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.109.01/parosci.nc INFO 2025-06-26 20:22:59,138 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:22:59,138 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.109.01/parosci.nc INFO 2025-06-26 20:22:59,141 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397932053.1, sensor_off_time = 1397943156.6 INFO 2025-06-26 20:22:59,141 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11103 seconds. Expecting to read 22206 L frames from the lopc.bin file. INFO 2025-06-26 20:22:59,141 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22206 records from the lopc.bin file. INFO 2025-06-26 20:22:59,272 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-19 18:27:33 Z and endTime = 2014-04-19 21:32:36 Z with 22206 records expected to be read from lopc.bin INFO 2025-06-26 20:22:59,272 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.109.01/lopc.bin INFO 2025-06-26 20:22:59,272 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.109.01/lopc.nc INFO 2025-06-26 20:22:59,273 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.109.01/lopc.nc INFO 2025-06-26 20:22:59,273 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.109.01 INFO 2025-06-26 20:22:59,274 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:22:59,277 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:22:59,356 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:22:59,356 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:22:59,356 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:22:59,530 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:22:59,530 process.py calibrate():227 [1] Calibration steps for 2014.109.01 INFO 2025-06-26 20:22:59,662 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 20:22:59,664 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:23:00,367 calibrate.py _nudge_pos():1806 [1] 109: 0.090 -0.0001355 -0.0001137 750 2.50 -8.373 -8.440 2014-04-19T18:31:46.001766144 INFO 2025-06-26 20:23:00,386 calibrate.py _nudge_pos():1806 [1] 111: 0.080 -0.0000107 0.0000003 85 0.28 -5.919 0.181 2014-04-19T18:32:04.000532992 INFO 2025-06-26 20:23:00,926 calibrate.py _nudge_pos():1806 [1] 169: 0.080 0.0007258 -0.0004344 7575 25.25 4.437 -3.188 2014-04-19T18:58:16.002843648 INFO 2025-06-26 20:23:01,454 calibrate.py _nudge_pos():1806 [1] 226: 0.080 0.0005080 -0.0002822 10880 36.26 2.162 -1.442 2014-04-19T19:35:28.009940736 INFO 2025-06-26 20:23:01,954 calibrate.py _nudge_pos():1806 [1] 280: 0.090 -0.0000601 -0.0001724 7415 24.71 -0.376 -1.293 2014-04-19T20:01:04.004717824 INFO 2025-06-26 20:23:02,551 calibrate.py _nudge_pos():1806 [1] 343: 0.090 -0.0017591 0.0004701 9530 31.76 -8.553 2.743 2014-04-19T20:33:52.009900288 INFO 2025-06-26 20:23:03,090 calibrate.py _nudge_pos():1806 [1] 401: 0.100 -0.0002777 0.0002351 7305 24.35 -1.762 1.789 2014-04-19T20:59:10.005910272 INFO 2025-06-26 20:23:03,415 calibrate.py _nudge_pos():1806 [1] 436: 0.110 0.0006373 0.0004077 9610 32.03 3.074 2.359 2014-04-19T21:31:46.001915392 INFO 2025-06-26 20:23:03,890 calibrate.py _nudge_pos():1862 [1] 444: - - - 3 0.01 - - INFO 2025-06-26 20:23:03,891 calibrate.py _nudge_pos():1868 [1] Points in final series = 55326 INFO 2025-06-26 20:23:04,398 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:23:04,822 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:23:05,151 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:23:05,153 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.109.01/ctd1.nc INFO 2025-06-26 20:23:05,154 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:23:05,154 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 20:23:05,154 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:23:05,550 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:23:05,880 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:23:05,882 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.109.01/ctd2.nc INFO 2025-06-26 20:23:05,883 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:23:05,883 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 20:23:05,883 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:23:05,905 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:23:06,442 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66] INFO 2025-06-26 20:23:06,540 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:23:16,527 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.109.01 ERROR 2025-06-26 20:23:16,528 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.109.01 INFO 2025-06-26 20:23:16,573 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_cal.nc INFO 2025-06-26 20:23:16,671 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 20:23:16,677 process.py align():251 [1] Alignment steps for 2014.109.01 INFO 2025-06-26 20:23:16,710 align.py process_cal():139 [1] Processing dorado_2014.109.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.109.01 INFO 2025-06-26 20:23:16,728 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:16,731 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:16,773 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:16,776 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:16,819 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:16,823 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:16,848 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:23:16,848 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:23:16,864 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:23:16,867 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:16,908 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:16,911 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:16,947 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:16,950 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:16,987 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:16,990 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,027 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,030 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,067 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,070 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,106 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,109 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,146 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,149 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,184 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,187 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,224 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,227 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,265 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,269 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,307 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,310 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,347 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,350 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,386 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,389 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,425 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,428 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,466 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,469 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,506 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,510 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,547 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,551 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,587 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,590 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,628 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,631 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,669 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,673 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,710 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,714 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,751 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.109.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:23:17,754 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:23:17,799 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:23:17,833 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:23:17,866 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:23:17,902 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:23:17,938 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:23:17,995 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:23:18,279 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:23:18,311 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_align.nc INFO 2025-06-26 20:23:18,414 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 20:23:18,416 process.py resample():273 [1] Resampling steps for 2014.109.01 INFO 2025-06-26 20:23:18,417 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:23:18,448 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_align.nc mission netCDF file INFO 2025-06-26 20:23:18,453 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_align.nc mission netCDF file INFO 2025-06-26 20:23:18,455 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-19T18:28:11.416466176 to 2014-04-19T21:32:36.608448768 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:23:18,456 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-19T18:27:38.968689152 to 2014-04-19T21:32:36.568451328 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 20:23:18,458 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-19T18:28:01.327157504 to 2014-04-19T21:32:36.578450688 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 20:23:18,459 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-19T18:28:01.057175808 to 2014-04-19T21:32:36.568451328 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 20:23:18,461 resample.py get_mission_start_end():1145 [1] isus : 2014-04-19T18:28:43.744251648 to 2014-04-19T21:32:36.528454400 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 20:23:18,462 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-19T18:27:30.969202688 to 2014-04-19T21:32:35.328502272 (0 days 00:00:01.279946496 before mission_end) INFO 2025-06-26 20:23:18,464 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-19T18:27:29.709323520 to 2014-04-19T21:32:36.418461696 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 20:23:18,464 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_align.nc mission netCDF file INFO 2025-06-26 20:23:18,465 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,595 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,619 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,643 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,667 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,688 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,709 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,730 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,750 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,769 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,788 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,811 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,830 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,848 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,867 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,885 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,904 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,923 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,943 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,962 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:18,982 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,002 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,023 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,043 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,063 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,075 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,087 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,098 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,108 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,117 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,121 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:23:19,121 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:23:19,501 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:23:19,568 resample.py add_biolume_proxies():633 [1] Zero flow values found: 11106 of 11106 - replaced with 350 ml/s INFO 2025-06-26 20:23:19,568 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:23:19,607 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:23:19,625 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:23:19,641 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:23:19,641 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:23:19,669 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:23:19,840 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_1S.nc INFO 2025-06-26 20:23:21,561 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:23:33,159 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.109.01/dorado_2014.109.01_1S_Gulper.txt INFO 2025-06-26 20:23:33,160 process.py archive():337 [1] Archiving steps for 2014.109.01 INFO 2025-06-26 20:23:33,160 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:23:33,161 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:23:33,162 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.109.01_1S.nc INFO 2025-06-26 20:23:33,179 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:23:33,180 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.109.01_cal.nc INFO 2025-06-26 20:23:33,258 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:23:33,259 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.109.01_align.nc INFO 2025-06-26 20:23:33,369 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:23:33,385 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,400 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,404 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,419 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,463 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,468 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,492 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,507 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,539 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,544 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014109/2014.109.01 done. INFO 2025-06-26 20:23:33,545 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:23:33,546 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.109.01_1S_Gulper.txt INFO 2025-06-26 20:23:33,550 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.109.01/dorado_2014.109.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:23:33,550 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.109.01/dorado_2014.109.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf