INFO 2025-06-26 10:45:41,163 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 10:45:41,163 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled 8/16/05 - ctdToUse = ctd1 INFO 2025-06-26 10:45:41,163 process.py process_mission():449 [1] Processing BIOLUME mission 2005.224.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:45:41,163 process.py download_process():165 [1] Download and processing steps for 2005.224.00 INFO 2025-06-26 10:45:41,163 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005224/2005.224.00 INFO 2025-06-26 10:45:41,163 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005224/2005.224.00 to /data/auv_data/dorado/missionlogs/2005.224.00 INFO 2025-06-26 10:45:41,906 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.224.00 INFO 2025-06-26 10:45:41,906 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/ctdDriver.log (9095019 bytes) INFO 2025-06-26 10:45:42,587 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/ctdDriver2.log (9095013 bytes) INFO 2025-06-26 10:45:43,286 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/gps.log (91148 bytes) INFO 2025-06-26 10:45:43,304 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/hydroscatlog.log (6204014 bytes) INFO 2025-06-26 10:45:44,058 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/navigation.log (30493686 bytes) INFO 2025-06-26 10:45:46,240 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/isuslog.log (557461 bytes) INFO 2025-06-26 10:45:46,296 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.224.00/isuslog.log: [1 2 3 4 5 6] INFO 2025-06-26 10:45:46,298 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/parosci.log (13272662 bytes) INFO 2025-06-26 10:45:47,449 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/tailCone.log (6207211 bytes) INFO 2025-06-26 10:45:48,209 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.224.00/biolume.log (7038412 bytes) INFO 2025-06-26 10:45:48,885 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:45:49,243 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.34 seconds WARNING 2025-06-26 10:45:49,243 process.py download_process():196 [1] No lopc.bin file for 2005.224.00 INFO 2025-06-26 10:45:49,243 process.py calibrate():227 [1] Calibration steps for 2005.224.00 INFO 2025-06-26 10:45:49,451 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 10:45:49,453 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:45:51,070 calibrate.py _nudge_pos():1806 [1] 184: 0.140 -0.0000557 -0.0002078 1795 5.98 -1.380 -6.440 2005-08-12T03:45:31.040991744 INFO 2025-06-26 10:45:52,049 calibrate.py _nudge_pos():1806 [1] 286: 0.130 -0.0007261 0.0004541 9425 31.41 -3.425 2.679 2005-08-12T04:18:37.044941184 INFO 2025-06-26 10:45:52,875 calibrate.py _nudge_pos():1806 [1] 370: 0.120 -0.0008308 0.0003634 9820 32.73 -3.762 2.057 2005-08-12T04:52:44.044712064 INFO 2025-06-26 10:45:53,906 calibrate.py _nudge_pos():1806 [1] 476: 0.140 -0.0013440 -0.0001417 10060 33.53 -5.944 -0.783 2005-08-12T05:28:01.039687808 INFO 2025-06-26 10:45:54,431 calibrate.py _nudge_pos():1806 [1] 529: 0.160 -0.0029319 0.0000409 10930 36.43 -11.939 0.208 2005-08-12T06:05:19.046374144 INFO 2025-06-26 10:45:55,332 calibrate.py _nudge_pos():1806 [1] 620: 0.140 -0.0021236 0.0007714 9990 33.30 -9.464 4.293 2005-08-12T06:40:07.043336448 INFO 2025-06-26 10:45:55,990 calibrate.py _nudge_pos():1806 [1] 688: 0.140 -0.0026292 0.0008440 10705 35.68 -10.939 4.383 2005-08-12T07:16:55.042078208 INFO 2025-06-26 10:45:56,794 calibrate.py _nudge_pos():1806 [1] 771: 0.140 -0.0008331 0.0002008 4600 15.33 -8.068 2.427 2005-08-12T07:33:37.043436288 INFO 2025-06-26 10:45:57,223 calibrate.py _nudge_pos():1806 [1] 815: 0.160 -0.0000116 -0.0000114 15 0.05 -36.932 -45.311 2005-08-12T07:34:23.040285312 INFO 2025-06-26 10:45:57,243 calibrate.py _nudge_pos():1806 [1] 817: 0.150 0.0001200 -0.0004814 10385 34.61 0.515 -2.577 2005-08-12T08:09:01.037932928 INFO 2025-06-26 10:45:57,809 calibrate.py _nudge_pos():1806 [1] 875: 0.150 0.0002109 -0.0005564 9765 32.55 0.963 -3.168 2005-08-12T08:42:31.040238080 INFO 2025-06-26 10:45:58,428 calibrate.py _nudge_pos():1806 [1] 938: 0.140 -0.0000499 -0.0003486 9830 32.76 -0.226 -1.972 2005-08-12T09:16:19.041310592 INFO 2025-06-26 10:45:58,950 calibrate.py _nudge_pos():1806 [1] 991: 0.150 -0.0000414 -0.0003399 10270 34.23 -0.180 -1.840 2005-08-12T09:51:25.037040000 INFO 2025-06-26 10:45:59,542 calibrate.py _nudge_pos():1806 [1] 1050: 0.140 -0.0000146 -0.0000565 10030 33.43 -0.065 -0.313 2005-08-12T10:25:49.045645696 INFO 2025-06-26 10:46:00,261 calibrate.py _nudge_pos():1806 [1] 1121: 0.140 -0.0000380 -0.0000174 2590 8.63 -0.654 -0.373 2005-08-12T10:35:37.045365120 INFO 2025-06-26 10:46:00,973 calibrate.py _nudge_pos():1806 [1] 1193: 0.160 0.0000364 0.0000000 2915 9.71 0.558 0.000 2005-08-12T10:46:31.040563328 INFO 2025-06-26 10:46:01,588 calibrate.py _nudge_pos():1862 [1] 1232: - - - 1 0.00 - - INFO 2025-06-26 10:46:01,588 calibrate.py _nudge_pos():1868 [1] Points in final series = 129201 WARNING 2025-06-26 10:46:01,875 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:46:02,836 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:46:03,823 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:46:04,599 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:46:04,602 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.224.00/ctd1.nc INFO 2025-06-26 10:46:04,603 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 10:46:04,604 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 10:46:04,604 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:46:05,528 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:46:06,300 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:46:06,302 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.224.00/ctd2.nc INFO 2025-06-26 10:46:06,303 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:46:06,304 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 10:46:06,304 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:46:07,144 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:46:08,339 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 37980 55560 55740 56100 56280 56460 56640 56880 170220 170400 171000 172320 172680 173100 173640 174000 174360 175920 281880 282060 285240 285420 303000 344460 346260 350340 391740 393360 394320 395340 397500 397680 397860 399420 399780 495420 511020 511200 513120 538560 538920 542700 543060 606960 623580 625080 625260 626460 627420 719160 732240 844800 847800 848940 957420 958620 960360 1001340 1001940 1004520 1071180 1074660 1076520 1077120 1113420 1114380 1116180 1185360 1186020 1189620 1190640 1194960 1300320 1301100 1301940 1306260 1410420 1410600 1413480 1413840 1414860 1415820 1419780 1467240 1468980 1469160 1525020 1525380 1525560 1527480 1529940 1530360] INFO 2025-06-26 10:46:08,592 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:46:08,598 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 10:46:08,599 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.224.00 ERROR 2025-06-26 10:46:08,599 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.224.00 INFO 2025-06-26 10:46:08,701 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_cal.nc INFO 2025-06-26 10:46:08,812 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 10:46:08,818 process.py align():251 [1] Alignment steps for 2005.224.00 INFO 2025-06-26 10:46:08,849 align.py process_cal():139 [1] Processing dorado_2005.224.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.224.00 INFO 2025-06-26 10:46:08,890 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:46:08,895 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:46:08,994 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:46:09,000 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:46:09,092 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:46:09,098 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:46:09,153 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:46:09,153 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:46:09,190 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:46:09,196 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:46:09,287 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:46:09,293 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,373 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:46:09,378 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,459 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:46:09,464 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,544 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:09,550 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,631 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:09,636 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,714 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:09,720 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,799 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:09,805 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,883 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:09,888 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:09,971 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:09,976 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,059 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,065 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,150 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,155 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,235 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,241 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,320 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,325 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,404 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,409 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,494 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,499 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,584 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,590 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,670 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,675 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,754 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,759 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,840 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,845 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:10,923 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.224.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:46:10,928 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:46:11,033 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:46:11,102 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:46:11,189 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:46:11,266 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:46:11,340 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:46:11,405 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_align.nc INFO 2025-06-26 10:46:11,494 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 10:46:11,496 process.py resample():273 [1] Resampling steps for 2005.224.00 INFO 2025-06-26 10:46:11,497 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:46:11,524 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_align.nc mission netCDF file INFO 2025-06-26 10:46:11,530 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_align.nc mission netCDF file INFO 2025-06-26 10:46:11,531 resample.py get_mission_start_end():1145 [1] navigation: 2005-08-12T03:36:51.056613248 to 2005-08-12T10:47:31.246438784 (0 days 00:00:00.069995392 before mission_end) INFO 2025-06-26 10:46:11,533 resample.py get_mission_start_end():1145 [1] hs2 : 2005-08-12T03:36:33.207835904 to 2005-08-12T10:47:31.316434176 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:46:11,535 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-08-12T03:36:55.766290432 to 2005-08-12T10:47:31.156445056 (0 days 00:00:00.159989120 before mission_end) INFO 2025-06-26 10:46:11,536 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-08-12T03:36:55.886282240 to 2005-08-12T10:47:31.296435328 (0 days 00:00:00.019998848 before mission_end) INFO 2025-06-26 10:46:11,538 resample.py get_mission_start_end():1145 [1] isus : 2005-08-12T03:37:31.013875968 to 2005-08-12T10:47:30.786470400 (0 days 00:00:00.529963776 before mission_end) INFO 2025-06-26 10:46:11,539 resample.py get_mission_start_end():1145 [1] biolume : 2005-08-12T03:36:28.248141312 to 2005-08-12T10:47:30.496455936 (0 days 00:00:00.819978240 before mission_end) INFO 2025-06-26 10:46:11,541 resample.py get_mission_start_end():1145 [1] tailcone : 2005-08-12T03:36:28.688145408 to 2005-08-12T10:47:31.246438784 (0 days 00:00:00.069995392 before mission_end) INFO 2025-06-26 10:46:11,542 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_align.nc mission netCDF file INFO 2025-06-26 10:46:11,542 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:11,817 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:11,864 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:11,911 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:11,957 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:11,997 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,039 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,080 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,120 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,157 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,194 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,232 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,269 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,306 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,342 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,379 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,416 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,457 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,496 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,535 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,574 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,614 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,653 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,671 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,687 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,701 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,719 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:12,763 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:46:13,004 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_1S.nc INFO 2025-06-26 10:46:14,104 create_products.py gulper_odv():401 [1] No gulper times found for 2005.224.00 INFO 2025-06-26 10:46:14,104 process.py archive():337 [1] Archiving steps for 2005.224.00 INFO 2025-06-26 10:46:14,104 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00, BASE_PATH = /data/auv_data INFO 2025-06-26 10:46:14,105 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:46:14,106 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.224.00_1S.nc INFO 2025-06-26 10:46:14,131 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:46:14,132 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.224.00_cal.nc INFO 2025-06-26 10:46:14,237 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:46:14,238 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.224.00_align.nc INFO 2025-06-26 10:46:14,344 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:46:14,374 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,402 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,407 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,429 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,520 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,528 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,567 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,592 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,663 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005224/2005.224.00 done. INFO 2025-06-26 10:46:14,663 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:46:14,663 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.224.00/dorado_2005.224.00_processing.log /Volumes/AUVCTD/surveys/2005/netcdf