INFO 2025-06-26 05:37:29,445 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2003 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 05:37:29,445 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 7/7/05 - ctdToUse = ctd1 INFO 2025-06-26 05:37:29,445 process.py process_mission():449 [1] Processing BIOLUME mission 2003.227.02 by user docker_user on host 671049448ece INFO 2025-06-26 05:37:29,445 process.py download_process():165 [1] Download and processing steps for 2003.227.02 INFO 2025-06-26 05:37:29,446 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2003/2003227/2003.227.02 INFO 2025-06-26 05:37:29,446 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2003/2003227/2003.227.02 to /data/auv_data/dorado/missionlogs/2003.227.02 INFO 2025-06-26 05:37:31,373 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2003.227.02 INFO 2025-06-26 05:37:31,373 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/ctdDriver.log (5970227 bytes) INFO 2025-06-26 05:37:31,813 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/ctdDriver2.log (5970221 bytes) INFO 2025-06-26 05:37:32,268 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/gps.log (30686 bytes) INFO 2025-06-26 05:37:32,279 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/hydroscatlog.log (4073114 bytes) INFO 2025-06-26 05:37:32,769 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/navigation.log (16620570 bytes) INFO 2025-06-26 05:37:34,024 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/isuslog.log (327125 bytes) INFO 2025-06-26 05:37:34,060 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/parosci.log (4075334 bytes) INFO 2025-06-26 05:37:34,419 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/tailCone.log (4075003 bytes) WARNING 2025-06-26 05:37:34,419 logs2netcdfs.py download_process_logs():795 [1] Failed to parse long_name & units from header in file /data/auv_data/dorado/missionlogs/2003.227.02/tailCone.log INFO 2025-06-26 05:37:34,420 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2003.227.02/biolume.log (4621664 bytes) INFO 2025-06-26 05:37:34,872 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 05:37:35,117 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.74 seconds WARNING 2025-06-26 05:37:35,117 process.py download_process():196 [1] No lopc.bin file for 2003.227.02 INFO 2025-06-26 05:37:35,118 process.py calibrate():227 [1] Calibration steps for 2003.227.02 INFO 2025-06-26 05:37:35,271 calibrate.py _navigation_process():1524 [1] Converting from Easting/Northing to lat/lon for mission 2003.227.02 INFO 2025-06-26 05:37:35,292 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 05:37:35,294 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 05:37:36,604 calibrate.py _nudge_pos():1806 [1] 153: 0.120 0.0000316 -0.0000463 30 0.10 48.712 -88.763 2003-08-15T06:34:58.384542080 INFO 2025-06-26 05:37:36,883 calibrate.py _nudge_pos():1806 [1] 182: 0.100 -0.0052604 0.0026442 13536 45.12 -17.351 10.860 2003-08-15T07:20:33.587167872 INFO 2025-06-26 05:37:37,210 calibrate.py _nudge_pos():1806 [1] 217: 0.100 0.0000201 -0.0000331 25 0.08 37.404 -76.757 2003-08-15T07:21:13.584427776 INFO 2025-06-26 05:37:37,278 calibrate.py _nudge_pos():1806 [1] 224: 0.090 -0.0000968 -0.0000688 75 0.25 -58.342 -51.628 2003-08-15T07:21:34.592988672 INFO 2025-06-26 05:37:37,298 calibrate.py _nudge_pos():1806 [1] 226: 0.090 -0.0000396 0.0000132 15 0.05 -126.186 52.410 2003-08-15T07:21:38.592714624 INFO 2025-06-26 05:37:37,337 calibrate.py _nudge_pos():1806 [1] 230: 0.090 -0.0000478 0.0000030 25 0.08 -88.839 6.870 2003-08-15T07:21:46.592166656 INFO 2025-06-26 05:37:37,347 calibrate.py _nudge_pos():1806 [1] 231: 0.090 0.0002416 0.0002433 20 0.06 567.636 711.778 2003-08-15T07:21:50.591892736 INFO 2025-06-26 05:37:37,358 calibrate.py _nudge_pos():1806 [1] 232: 0.080 -0.0067514 -0.0027469 13656 45.52 -22.067 -11.183 2003-08-15T08:07:21.784793088 INFO 2025-06-26 05:37:37,793 calibrate.py _nudge_pos():1806 [1] 278: 0.070 -0.0000042 -0.0000821 40 0.13 -4.820 -117.069 2003-08-15T08:08:15.791093504 INFO 2025-06-26 05:37:37,871 calibrate.py _nudge_pos():1806 [1] 286: 0.070 -0.0056351 -0.0061688 13641 45.47 -18.434 -25.141 2003-08-15T08:53:51.993650816 INFO 2025-06-26 05:37:38,110 calibrate.py _nudge_pos():1806 [1] 311: 0.070 -0.0000421 -0.0000286 35 0.11 -55.262 -46.783 2003-08-15T08:54:22.991527168 INFO 2025-06-26 05:37:38,283 calibrate.py _nudge_pos():1806 [1] 329: 0.070 -0.0000624 -0.0000034 20 0.06 -146.632 -9.878 2003-08-15T08:54:43.990088704 INFO 2025-06-26 05:37:38,314 calibrate.py _nudge_pos():1806 [1] 332: 0.070 -0.0001503 0.0000052 75 0.25 -90.663 3.900 2003-08-15T08:55:00.988924288 INFO 2025-06-26 05:37:38,390 calibrate.py _nudge_pos():1806 [1] 340: 0.070 -0.0000406 -0.0000044 20 0.06 -95.436 -12.832 2003-08-15T08:55:13.988033792 INFO 2025-06-26 05:37:38,400 calibrate.py _nudge_pos():1806 [1] 341: 0.030 -0.0042097 -0.0069188 13861 46.20 -13.549 -27.750 2003-08-15T09:41:26.188125056 INFO 2025-06-26 05:37:38,847 calibrate.py _nudge_pos():1806 [1] 388: 0.040 0.0000218 0.0000971 40 0.13 24.901 138.377 2003-08-15T09:42:21.184357504 INFO 2025-06-26 05:37:38,982 calibrate.py _nudge_pos():1806 [1] 402: 0.030 0.0000348 0.0000447 20 0.06 81.731 130.788 2003-08-15T09:42:39.193123840 INFO 2025-06-26 05:37:39,030 calibrate.py _nudge_pos():1806 [1] 407: 0.020 -0.0048525 -0.0071079 13671 45.57 -15.831 -28.905 2003-08-15T10:28:17.385544832 INFO 2025-06-26 05:37:39,678 calibrate.py _nudge_pos():1806 [1] 476: 0.190 -0.0051559 -0.0063186 13660 45.53 -16.829 -25.716 2003-08-15T11:14:58.393662592 INFO 2025-06-26 05:37:39,891 calibrate.py _nudge_pos():1862 [1] 478: - - - 0 0.00 - - INFO 2025-06-26 05:37:39,891 calibrate.py _nudge_pos():1868 [1] Points in final series = 84787 WARNING 2025-06-26 05:37:39,960 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 05:37:40,587 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:41,224 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:41,717 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:41,719 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2003.227.02/ctd1.nc INFO 2025-06-26 05:37:41,720 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 05:37:41,720 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 05:37:41,720 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 05:37:42,311 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:42,810 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 05:37:42,813 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2003.227.02/ctd2.nc INFO 2025-06-26 05:37:42,814 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 05:37:42,814 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 05:37:42,815 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 05:37:42,842 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 05:37:43,631 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 780 960 36180 37560 56580 130620 147720 160980 189300 191280 192480 218760 225840 228180 231000 262620 263160 277020 391080 399360 511620 529320 548760 550320 554160 624060 640980 686160 763920 774300 800700 923940 940980 955020 1001400] INFO 2025-06-26 05:37:43,776 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 05:37:43,782 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 05:37:43,782 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2003.227.02 ERROR 2025-06-26 05:37:43,783 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2003.227.02 ERROR 2025-06-26 05:37:43,783 calibrate.py process_logs():3542 [1] Error processing tailcone: tailcone has no orig_data - likely a missing or zero-sized .log file in missionlogs/2003.227.02 INFO 2025-06-26 05:37:43,783 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_cal.nc INFO 2025-06-26 05:37:43,858 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, time INFO 2025-06-26 05:37:43,861 process.py align():251 [1] Alignment steps for 2003.227.02 INFO 2025-06-26 05:37:43,886 align.py process_cal():139 [1] Processing dorado_2003.227.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2003.227.02 INFO 2025-06-26 05:37:43,913 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:37:43,916 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:37:43,980 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:37:43,985 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:37:44,047 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:37:44,051 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:37:44,088 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 05:37:44,088 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 05:37:44,113 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 05:37:44,117 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 05:37:44,179 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:37:44,183 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,237 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:37:44,241 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,298 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 05:37:44,302 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,355 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,359 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,414 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,418 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,472 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,476 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,531 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,535 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,590 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,593 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,648 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,652 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,705 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,710 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,766 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,770 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,824 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,828 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,882 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,885 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:44,940 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:44,944 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,000 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:45,004 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,059 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:45,063 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,118 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:45,121 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,176 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:45,180 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,234 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:45,238 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,294 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2003.227.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 05:37:45,297 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 05:37:45,358 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.60 INFO 2025-06-26 05:37:45,398 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.60 INFO 2025-06-26 05:37:45,437 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.60 INFO 2025-06-26 05:37:45,479 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 05:37:45,496 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_align.nc INFO 2025-06-26 05:37:45,560 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 INFO 2025-06-26 05:37:45,562 process.py resample():273 [1] Resampling steps for 2003.227.02 INFO 2025-06-26 05:37:45,563 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 05:37:45,585 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_align.nc mission netCDF file INFO 2025-06-26 05:37:45,590 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_align.nc mission netCDF file INFO 2025-06-26 05:37:45,591 resample.py get_mission_start_end():1145 [1] navigation: 2003-08-15T06:32:42.193871744 to 2003-08-15T11:15:20.602141312 (0 days 00:00:00.109992320 before mission_end) INFO 2025-06-26 05:37:45,593 resample.py get_mission_start_end():1145 [1] hs2 : 2003-08-15T06:32:24.385091840 to 2003-08-15T11:15:20.712133632 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:37:45,594 resample.py get_mission_start_end():1145 [1] ctd1 : 2003-08-15T06:32:40.274003328 to 2003-08-15T11:15:20.712133632 (0 days 00:00:00 before mission_end) INFO 2025-06-26 05:37:45,596 resample.py get_mission_start_end():1145 [1] ctd2 : 2003-08-15T06:32:40.503987584 to 2003-08-15T11:15:20.672136448 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 05:37:45,597 resample.py get_mission_start_end():1145 [1] isus : 2003-08-15T06:33:36.380159744 to 2003-08-15T11:15:19.062246656 (0 days 00:00:01.649886976 before mission_end) INFO 2025-06-26 05:37:45,598 resample.py get_mission_start_end():1145 [1] biolume : 2003-08-15T06:32:18.765442432 to 2003-08-15T11:15:19.352192640 (0 days 00:00:01.359940992 before mission_end) INFO 2025-06-26 05:37:45,599 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_align.nc mission netCDF file INFO 2025-06-26 05:37:45,599 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,785 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,818 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,851 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,883 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,912 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,941 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,969 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:45,997 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,024 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,049 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,075 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,100 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,126 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,152 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,178 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,203 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,231 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,261 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,289 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,316 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,343 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,371 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,385 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,398 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,409 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,423 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 05:37:46,605 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_1S.nc INFO 2025-06-26 05:37:47,959 create_products.py gulper_odv():401 [1] No gulper times found for 2003.227.02 INFO 2025-06-26 05:37:47,959 process.py archive():337 [1] Archiving steps for 2003.227.02 INFO 2025-06-26 05:37:47,959 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02, BASE_PATH = /data/auv_data INFO 2025-06-26 05:37:47,961 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02 files to /Volumes/AUVCTD/surveys/2003/netcdf INFO 2025-06-26 05:37:47,962 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2003/netcdf/dorado_2003.227.02_1S.nc INFO 2025-06-26 05:37:47,980 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_1S.nc /Volumes/AUVCTD/surveys/2003/netcdf done. INFO 2025-06-26 05:37:47,981 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2003/netcdf/dorado_2003.227.02_cal.nc INFO 2025-06-26 05:37:48,049 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_cal.nc /Volumes/AUVCTD/surveys/2003/netcdf done. INFO 2025-06-26 05:37:48,050 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2003/netcdf/dorado_2003.227.02_align.nc INFO 2025-06-26 05:37:48,119 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_align.nc /Volumes/AUVCTD/surveys/2003/netcdf done. INFO 2025-06-26 05:37:48,148 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,174 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,179 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,197 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,255 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,261 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,278 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,332 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2003/2003227/2003.227.02 done. INFO 2025-06-26 05:37:48,332 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 05:37:48,333 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2003.227.02/dorado_2003.227.02_processing.log /Volumes/AUVCTD/surveys/2003/netcdf