INFO 2025-06-26 10:59:51,813 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 10:59:51,813 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled by DMO 9/16/05 - ctdToUse = ctd1 INFO 2025-06-26 10:59:51,813 process.py process_mission():449 [1] Processing BIOLUME mission 2005.259.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:59:51,813 process.py download_process():165 [1] Download and processing steps for 2005.259.00 INFO 2025-06-26 10:59:51,813 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005259/2005.259.00 INFO 2025-06-26 10:59:51,813 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005259/2005.259.00 to /data/auv_data/dorado/missionlogs/2005.259.00 INFO 2025-06-26 10:59:55,209 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.259.00 INFO 2025-06-26 10:59:55,209 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/ctdDriver.log (9283427 bytes) INFO 2025-06-26 10:59:55,919 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/ctdDriver2.log (9283421 bytes) INFO 2025-06-26 10:59:56,596 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/gps.log (81428 bytes) INFO 2025-06-26 10:59:56,613 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/hydroscatlog.log (6333074 bytes) INFO 2025-06-26 10:59:57,368 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.259.00/hydroscatlog.log: [3008] INFO 2025-06-26 10:59:57,385 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/navigation.log (31124514 bytes) INFO 2025-06-26 10:59:59,582 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/isuslog.log (532149 bytes) INFO 2025-06-26 10:59:59,637 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/parosci.log (13552502 bytes) INFO 2025-06-26 11:00:00,730 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.259.00/parosci.log: [ 8037 8038 8060 8061 123171] INFO 2025-06-26 11:00:00,765 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/tailCone.log (6334987 bytes) INFO 2025-06-26 11:00:01,564 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.259.00/biolume.log (7184748 bytes) INFO 2025-06-26 11:00:02,253 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:00:02,628 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.42 seconds WARNING 2025-06-26 11:00:02,628 process.py download_process():196 [1] No lopc.bin file for 2005.259.00 INFO 2025-06-26 11:00:02,628 process.py calibrate():227 [1] Calibration steps for 2005.259.00 INFO 2025-06-26 11:00:02,852 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 11:00:02,854 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:00:04,506 calibrate.py _nudge_pos():1806 [1] 183: 0.030 -0.0001508 0.0000068 2640 8.80 -2.539 0.143 2005-09-16T02:19:49.079940992 INFO 2025-06-26 11:00:05,333 calibrate.py _nudge_pos():1806 [1] 268: 0.050 -0.0003487 0.0002425 9970 33.23 -1.555 1.352 2005-09-16T02:54:27.077588352 INFO 2025-06-26 11:00:06,097 calibrate.py _nudge_pos():1806 [1] 347: 0.040 -0.0006686 0.0002668 10550 35.16 -2.818 1.406 2005-09-16T03:30:55.077700096 INFO 2025-06-26 11:00:06,812 calibrate.py _nudge_pos():1806 [1] 422: 0.030 -0.0015412 0.0001321 10160 33.86 -6.749 0.723 2005-09-16T04:06:01.083428864 INFO 2025-06-26 11:00:07,430 calibrate.py _nudge_pos():1806 [1] 483: 0.040 -0.0046393 -0.0008668 10710 35.70 -19.279 -4.499 2005-09-16T04:42:43.082581504 INFO 2025-06-26 11:00:07,961 calibrate.py _nudge_pos():1806 [1] 536: 0.040 -0.0024100 -0.0009779 10840 36.13 -9.899 -5.015 2005-09-16T05:19:43.080501376 INFO 2025-06-26 11:00:08,613 calibrate.py _nudge_pos():1806 [1] 602: 0.060 -0.0010075 -0.0019167 10805 36.01 -4.153 -9.862 2005-09-16T05:56:49.078010112 INFO 2025-06-26 11:00:09,145 calibrate.py _nudge_pos():1806 [1] 655: 0.050 -0.0004814 -0.0009586 4510 15.03 -4.755 -11.818 2005-09-16T06:12:43.082656128 INFO 2025-06-26 11:00:09,746 calibrate.py _nudge_pos():1806 [1] 713: 0.040 0.0007197 -0.0023368 10820 36.06 2.964 -12.007 2005-09-16T06:49:44.080507520 INFO 2025-06-26 11:00:10,377 calibrate.py _nudge_pos():1806 [1] 773: 0.050 0.0006895 -0.0015049 9750 32.50 3.152 -8.581 2005-09-16T07:23:13.082881408 INFO 2025-06-26 11:00:11,000 calibrate.py _nudge_pos():1806 [1] 835: 0.040 0.0000666 -0.0003351 9775 32.58 0.304 -1.906 2005-09-16T07:56:49.084775680 INFO 2025-06-26 11:00:11,579 calibrate.py _nudge_pos():1806 [1] 893: 0.050 -0.0000559 -0.0001767 10215 34.05 -0.244 -0.962 2005-09-16T08:31:49.080916224 INFO 2025-06-26 11:00:12,094 calibrate.py _nudge_pos():1806 [1] 945: 0.050 -0.0001203 -0.0000386 10035 33.45 -0.535 -0.214 2005-09-16T09:06:07.079933696 INFO 2025-06-26 11:00:12,808 calibrate.py _nudge_pos():1806 [1] 1015: 0.050 -0.0000214 0.0002101 2595 8.65 -0.368 4.502 2005-09-16T09:15:55.079652736 INFO 2025-06-26 11:00:13,447 calibrate.py _nudge_pos():1806 [1] 1077: 0.050 -0.0000652 -0.0000095 3115 10.38 -0.934 -0.170 2005-09-16T09:27:19.082795392 INFO 2025-06-26 11:00:13,877 calibrate.py _nudge_pos():1862 [1] 1095: - - - 4 0.01 - - INFO 2025-06-26 11:00:13,877 calibrate.py _nudge_pos():1868 [1] Points in final series = 131873 WARNING 2025-06-26 11:00:18,524 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:00:32,848 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:00:33,915 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:00:34,737 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:00:34,740 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.259.00/ctd1.nc INFO 2025-06-26 11:00:34,741 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 11:00:34,741 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 11:00:34,741 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:00:35,728 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:00:36,548 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 11:00:36,551 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.259.00/ctd2.nc INFO 2025-06-26 11:00:36,552 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 11:00:36,553 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 11:00:36,553 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:00:36,592 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:00:37,812 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 45540 45541 45542 45543 45544 45545 45546 45547 45548 45549 45550 45551 45552 45553 108660 666000 883620 883920 1016580 1124760 1351020 1507620 1507621] INFO 2025-06-26 11:00:38,057 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:00:38,063 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 11:00:38,064 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.259.00 ERROR 2025-06-26 11:00:38,064 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.259.00 INFO 2025-06-26 11:00:38,168 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_cal.nc INFO 2025-06-26 11:00:38,279 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 11:00:38,283 process.py align():251 [1] Alignment steps for 2005.259.00 INFO 2025-06-26 11:00:38,315 align.py process_cal():139 [1] Processing dorado_2005.259.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.259.00 INFO 2025-06-26 11:00:38,352 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:00:38,357 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:00:38,451 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:00:38,456 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:00:38,548 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:00:38,553 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:00:38,610 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:00:38,610 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:00:38,646 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:00:38,652 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:00:38,739 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:00:38,744 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:38,823 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:00:38,828 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:38,907 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:00:38,911 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:38,989 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:38,994 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,075 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,080 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,161 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,167 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,247 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,252 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,331 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,336 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,416 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,421 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,501 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,507 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,585 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,590 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,685 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,690 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,770 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,775 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,859 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,864 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:39,948 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:39,954 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:40,041 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:40,047 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:40,134 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:40,139 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:40,220 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:40,226 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:40,308 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:40,313 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:40,396 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:00:40,401 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:00:40,508 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:00:40,589 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:00:40,657 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:00:40,729 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:00:40,803 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:00:40,867 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_align.nc INFO 2025-06-26 11:00:40,960 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 11:00:40,963 process.py resample():273 [1] Resampling steps for 2005.259.00 INFO 2025-06-26 11:00:40,963 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:00:40,991 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_align.nc mission netCDF file INFO 2025-06-26 11:00:40,997 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_align.nc mission netCDF file INFO 2025-06-26 11:00:40,999 resample.py get_mission_start_end():1145 [1] navigation: 2005-09-16T02:08:21.697029888 to 2005-09-16T09:28:00.879932160 (0 days 00:00:00.159988864 before mission_end) INFO 2025-06-26 11:00:41,001 resample.py get_mission_start_end():1145 [1] hs2 : 2005-09-16T02:08:04.808187008 to 2005-09-16T09:28:00.949927296 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 11:00:41,003 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-09-16T02:08:27.846608640 to 2005-09-16T09:28:00.969925888 (0 days 00:00:00.069995136 before mission_end) INFO 2025-06-26 11:00:41,005 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-09-16T02:08:27.906604544 to 2005-09-16T09:28:01.039921024 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:00:41,007 resample.py get_mission_start_end():1145 [1] isus : 2005-09-16T02:09:25.042690560 to 2005-09-16T09:28:00.979925120 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 11:00:41,008 resample.py get_mission_start_end():1145 [1] biolume : 2005-09-16T02:07:59.978483456 to 2005-09-16T09:28:00.159947136 (0 days 00:00:00.879973888 before mission_end) INFO 2025-06-26 11:00:41,010 resample.py get_mission_start_end():1145 [1] tailcone : 2005-09-16T02:08:00.218501376 to 2005-09-16T09:28:01.029921792 (0 days 00:00:00.009999232 before mission_end) INFO 2025-06-26 11:00:41,011 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_align.nc mission netCDF file INFO 2025-06-26 11:00:41,012 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,294 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,342 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,390 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,437 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,479 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,520 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,560 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,601 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,639 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,679 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,716 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,754 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,791 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,828 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,865 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,903 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,943 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:41,985 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,026 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,066 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,107 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,147 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,165 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,181 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,197 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,216 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,261 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:00:42,509 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_1S.nc INFO 2025-06-26 11:00:44,482 create_products.py gulper_odv():401 [1] No gulper times found for 2005.259.00 INFO 2025-06-26 11:00:44,483 process.py archive():337 [1] Archiving steps for 2005.259.00 INFO 2025-06-26 11:00:44,483 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00, BASE_PATH = /data/auv_data INFO 2025-06-26 11:00:44,488 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 11:00:44,489 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.259.00_1S.nc INFO 2025-06-26 11:00:44,514 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 11:00:44,515 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.259.00_cal.nc INFO 2025-06-26 11:00:44,645 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 11:00:44,646 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.259.00_align.nc INFO 2025-06-26 11:00:44,749 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 11:00:44,782 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:44,812 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:44,818 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:44,843 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:44,938 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:44,948 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:44,990 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:45,017 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:45,094 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005259/2005.259.00 done. INFO 2025-06-26 11:00:45,094 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:00:45,094 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.259.00/dorado_2005.259.00_processing.log /Volumes/AUVCTD/surveys/2005/netcdf