INFO 2025-06-26 11:07:20,399 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 11:07:20,399 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portal by Duane on 2/23/06 failed, executed from Eclipse to get through ingest/ruminate - multiple Ruminate problem - ctdToUse = ctd1 INFO 2025-06-26 11:07:20,399 process.py process_mission():449 [1] Processing BIOLUME mission 2006.054.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:07:20,399 process.py download_process():165 [1] Download and processing steps for 2006.054.00 INFO 2025-06-26 11:07:20,399 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006054/2006.054.00 INFO 2025-06-26 11:07:20,399 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006054/2006.054.00 to /data/auv_data/dorado/missionlogs/2006.054.00 INFO 2025-06-26 11:07:23,123 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.054.00 INFO 2025-06-26 11:07:23,124 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/ctdDriver.log (7704531 bytes) INFO 2025-06-26 11:07:23,691 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/ctdDriver2.log (7704525 bytes) INFO 2025-06-26 11:07:24,270 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/gps.log (308876 bytes) INFO 2025-06-26 11:07:24,312 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/hydroscatlog.log (5256374 bytes) INFO 2025-06-26 11:07:24,933 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/navigation.log (25833158 bytes) INFO 2025-06-26 11:07:26,762 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/isuslog.log (45077 bytes) INFO 2025-06-26 11:07:26,772 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/parosci.log (11248694 bytes) INFO 2025-06-26 11:07:27,711 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/tailCone.log (5259115 bytes) INFO 2025-06-26 11:07:28,381 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.054.00/biolume.log (5963740 bytes) INFO 2025-06-26 11:07:28,950 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:07:29,269 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.14 seconds WARNING 2025-06-26 11:07:29,269 process.py download_process():196 [1] No lopc.bin file for 2006.054.00 INFO 2025-06-26 11:07:29,269 process.py calibrate():227 [1] Calibration steps for 2006.054.00 INFO 2025-06-26 11:07:29,453 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 11:07:29,455 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:07:31,067 calibrate.py _nudge_pos():1806 [1] 185: 0.180 -0.0000150 0.0002081 1120 3.73 -0.596 10.337 2006-02-23T02:21:33.431518592 INFO 2025-06-26 11:07:32,174 calibrate.py _nudge_pos():1806 [1] 301: 0.180 -0.0036406 0.0019110 10255 34.18 -15.782 10.360 2006-02-23T02:57:39.433137152 INFO 2025-06-26 11:07:32,791 calibrate.py _nudge_pos():1806 [1] 366: 0.180 -0.0036532 0.0015031 10359 34.53 -15.684 8.067 2006-02-23T03:33:15.436811008 INFO 2025-06-26 11:07:33,457 calibrate.py _nudge_pos():1806 [1] 432: 0.190 -0.0044682 0.0007871 10265 34.21 -19.366 4.263 2006-02-23T04:08:33.431718400 INFO 2025-06-26 11:07:34,100 calibrate.py _nudge_pos():1806 [1] 498: 0.190 -0.0059152 -0.0018690 11315 37.71 -23.267 -9.183 2006-02-23T04:47:21.432239232 INFO 2025-06-26 11:07:34,663 calibrate.py _nudge_pos():1806 [1] 556: 0.200 -0.0040190 -0.0014751 10155 33.85 -17.621 -8.075 2006-02-23T05:22:09.429201792 INFO 2025-06-26 11:07:35,259 calibrate.py _nudge_pos():1806 [1] 615: 0.200 -0.0034817 0.0008501 2950 9.83 -52.565 16.024 2006-02-23T05:32:57.434810368 INFO 2025-06-26 11:07:35,462 calibrate.py _nudge_pos():1806 [1] 636: 0.010 -0.0033917 0.0006144 2489 8.30 -60.673 13.722 2006-02-23T05:41:35.629311616 INFO 2025-06-26 11:07:35,521 calibrate.py _nudge_pos():1806 [1] 642: 0.200 -0.0041989 0.0008651 2784 9.28 -67.181 17.280 2006-02-23T05:50:57.430825472 INFO 2025-06-26 11:07:35,608 calibrate.py _nudge_pos():1806 [1] 651: 0.010 -0.0047396 0.0012429 2451 8.17 -86.144 28.200 2006-02-23T05:59:15.636696064 INFO 2025-06-26 11:07:35,723 calibrate.py _nudge_pos():1806 [1] 663: 0.200 -0.0051281 0.0008331 2434 8.11 -93.864 19.034 2006-02-23T06:07:33.432594816 INFO 2025-06-26 11:07:36,432 calibrate.py _nudge_pos():1806 [1] 735: 0.200 -0.0042825 0.0012017 2704 9.01 -70.561 24.714 2006-02-23T06:17:45.430670080 INFO 2025-06-26 11:07:36,548 calibrate.py _nudge_pos():1806 [1] 747: 0.010 -0.0071396 0.0024810 4385 14.61 -72.533 31.459 2006-02-23T06:32:33.629824128 INFO 2025-06-26 11:07:37,209 calibrate.py _nudge_pos():1806 [1] 815: 0.200 -0.0078563 0.0006134 2874 9.58 -121.799 11.868 2006-02-23T06:43:15.435857536 INFO 2025-06-26 11:07:37,286 calibrate.py _nudge_pos():1806 [1] 823: 0.010 -0.0130011 0.0015294 4285 14.28 -135.183 19.846 2006-02-23T06:57:39.636655744 INFO 2025-06-26 11:07:37,326 calibrate.py _nudge_pos():1806 [1] 827: 0.010 -0.0040264 -0.0028185 2715 9.05 -66.090 -57.732 2006-02-23T07:06:45.629252736 INFO 2025-06-26 11:07:37,535 calibrate.py _nudge_pos():1806 [1] 848: 0.200 -0.0000679 -0.0011741 4699 15.66 -0.644 -13.893 2006-02-23T07:22:45.433501440 INFO 2025-06-26 11:08:07,345 calibrate.py _nudge_pos():1806 [1] 3837: 0.010 -0.0000064 -0.0000084 15 0.05 -20.461 -33.496 2006-02-23T08:12:36.628590592 INFO 2025-06-26 11:08:11,736 calibrate.py _nudge_pos():1862 [1] 4256: - - - 0 0.00 - - INFO 2025-06-26 11:08:11,736 calibrate.py _nudge_pos():1868 [1] Points in final series = 109050 INFO 2025-06-26 11:08:11,909 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=150) for self.args.mission=2006.054.00 INFO 2025-06-26 11:08:11,913 calibrate.py _depth_process():2175 [1] Setting 5 depths values to NaN WARNING 2025-06-26 11:08:11,917 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:08:12,736 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:08:13,570 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:08:14,230 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:08:14,233 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.054.00/ctd1.nc WARNING 2025-06-26 11:08:14,234 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (2034) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 11:08:14,234 calibrate.py _range_qc_combined_nc():898 [1] Setting 2034 ctd1_salinity values to NaN INFO 2025-06-26 11:08:14,234 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 11:08:14,234 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:08:15,016 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:08:15,675 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:08:15,677 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.054.00/ctd2.nc WARNING 2025-06-26 11:08:15,678 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (2030) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 11:08:15,679 calibrate.py _range_qc_combined_nc():898 [1] Setting 2030 ctd2_salinity values to NaN INFO 2025-06-26 11:08:15,679 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 11:08:15,679 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:08:15,703 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:08:16,704 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 76620 188700 190020 298560 301860] INFO 2025-06-26 11:08:16,906 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:08:16,912 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 11:08:16,912 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.054.00 ERROR 2025-06-26 11:08:16,912 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.054.00 INFO 2025-06-26 11:08:16,999 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_cal.nc INFO 2025-06-26 11:08:17,096 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 11:08:17,101 process.py align():251 [1] Alignment steps for 2006.054.00 INFO 2025-06-26 11:08:17,129 align.py process_cal():139 [1] Processing dorado_2006.054.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.054.00 INFO 2025-06-26 11:08:17,161 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:08:17,164 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:08:17,248 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:08:17,253 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:08:17,331 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:08:17,336 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:08:17,384 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:08:17,384 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:08:17,416 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:08:17,421 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:08:17,496 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:08:17,501 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:17,568 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:08:17,573 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:17,643 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:08:17,647 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:17,714 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:17,718 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:17,787 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:17,791 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:17,859 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:17,863 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:17,932 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:17,936 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,007 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,011 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,080 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,084 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,161 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,167 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,245 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,249 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,319 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,324 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,394 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,398 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,466 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,471 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,541 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,546 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,614 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,620 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,690 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,694 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,764 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,769 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,841 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,846 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:18,914 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.054.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:08:18,918 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:08:19,007 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.06 INFO 2025-06-26 11:08:19,061 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.06 INFO 2025-06-26 11:08:19,121 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.06 INFO 2025-06-26 11:08:19,178 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:08:19,244 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:08:19,298 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_align.nc INFO 2025-06-26 11:08:19,380 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 11:08:19,383 process.py resample():273 [1] Resampling steps for 2006.054.00 INFO 2025-06-26 11:08:19,383 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:08:19,409 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_align.nc mission netCDF file INFO 2025-06-26 11:08:19,415 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_align.nc mission netCDF file INFO 2025-06-26 11:08:19,416 resample.py get_mission_start_end():1145 [1] navigation: 2006-02-23T02:15:07.637947136 to 2006-02-23T08:19:58.628311680 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 11:08:19,418 resample.py get_mission_start_end():1145 [1] hs2 : 2006-02-23T02:14:50.879095296 to 2006-02-23T08:19:58.448323968 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 11:08:19,419 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-02-23T02:15:13.267561472 to 2006-02-23T08:19:58.508319872 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 11:08:19,421 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-02-23T02:15:13.417551232 to 2006-02-23T08:19:58.658309504 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:08:19,423 resample.py get_mission_start_end():1145 [1] isus : 2006-02-23T02:16:29.262355584 to 2006-02-23T08:19:58.418325888 (0 days 00:00:00.239983616 before mission_end) INFO 2025-06-26 11:08:19,424 resample.py get_mission_start_end():1145 [1] biolume : 2006-02-23T02:14:45.949398784 to 2006-02-23T08:19:57.618346496 (0 days 00:00:01.039963008 before mission_end) INFO 2025-06-26 11:08:19,426 resample.py get_mission_start_end():1145 [1] tailcone : 2006-02-23T02:14:46.249412352 to 2006-02-23T08:19:58.608313088 (0 days 00:00:00.049996416 before mission_end) INFO 2025-06-26 11:08:19,426 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_align.nc mission netCDF file INFO 2025-06-26 11:08:19,427 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,667 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,710 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,750 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,791 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,828 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,865 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,900 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,935 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:19,968 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,010 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,044 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,077 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,110 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,143 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,175 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,207 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,241 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,275 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,314 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,350 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,385 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,421 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,434 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,446 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,456 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,471 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,510 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:08:20,730 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_1S.nc INFO 2025-06-26 11:08:22,270 create_products.py gulper_odv():401 [1] No gulper times found for 2006.054.00 INFO 2025-06-26 11:08:22,270 process.py archive():337 [1] Archiving steps for 2006.054.00 INFO 2025-06-26 11:08:22,270 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00, BASE_PATH = /data/auv_data INFO 2025-06-26 11:08:22,272 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:08:22,273 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.054.00_1S.nc INFO 2025-06-26 11:08:22,294 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:08:22,295 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.054.00_cal.nc INFO 2025-06-26 11:08:22,388 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:08:22,389 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.054.00_align.nc INFO 2025-06-26 11:08:22,474 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:08:22,502 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,526 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,531 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,549 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,622 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,627 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,660 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,684 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,754 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006054/2006.054.00 done. INFO 2025-06-26 11:08:22,754 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:08:22,754 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.054.00/dorado_2006.054.00_processing.log /Volumes/AUVCTD/surveys/2006/netcdf