INFO 2025-06-26 06:12:05,819 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 06:12:05,819 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/22/05 - ctdToUse = ctd1 INFO 2025-06-26 06:12:05,819 process.py process_mission():449 [1] Processing BIOLUME mission 2004.352.00 by user docker_user on host 671049448ece INFO 2025-06-26 06:12:05,819 process.py download_process():165 [1] Download and processing steps for 2004.352.00 INFO 2025-06-26 06:12:05,819 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004352/2004.352.00 INFO 2025-06-26 06:12:05,820 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004352/2004.352.00 to /data/auv_data/dorado/missionlogs/2004.352.00 INFO 2025-06-26 06:12:07,933 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.352.00 INFO 2025-06-26 06:12:07,933 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/ctdDriver.log (6737587 bytes) INFO 2025-06-26 06:12:08,428 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/ctdDriver2.log (6663045 bytes) INFO 2025-06-26 06:12:08,896 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.352.00/ctdDriver2.log: [19541] INFO 2025-06-26 06:12:08,917 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/gps.log (66380 bytes) INFO 2025-06-26 06:12:08,934 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/hydroscatlog.log (4597454 bytes) INFO 2025-06-26 06:12:09,482 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.352.00/hydroscatlog.log: [52688] INFO 2025-06-26 06:12:09,493 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/navigation.log (14934043 bytes) INFO 2025-06-26 06:12:10,581 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/isuslog.log (395381 bytes) INFO 2025-06-26 06:12:10,623 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/parosci.log (4598726 bytes) INFO 2025-06-26 06:12:11,011 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/tailCone.log (4599979 bytes) INFO 2025-06-26 06:12:11,597 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.352.00/biolume.log (5216828 bytes) INFO 2025-06-26 06:12:12,097 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 06:12:12,377 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.44 seconds WARNING 2025-06-26 06:12:12,377 process.py download_process():196 [1] No lopc.bin file for 2004.352.00 INFO 2025-06-26 06:12:12,377 process.py calibrate():227 [1] Calibration steps for 2004.352.00 INFO 2025-06-26 06:12:12,546 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 06:12:12,548 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 06:12:14,114 calibrate.py _nudge_pos():1806 [1] 184: 0.060 -0.0000752 0.0000406 750 2.50 -4.459 3.016 2004-12-17T01:22:48.727323520 INFO 2025-06-26 06:12:14,910 calibrate.py _nudge_pos():1806 [1] 269: 0.080 -0.0015530 0.0006952 9870 32.90 -6.995 3.916 2004-12-17T01:57:06.726340992 INFO 2025-06-26 06:12:15,486 calibrate.py _nudge_pos():1806 [1] 329: 0.070 -0.0014176 0.0006010 9933 33.11 -6.346 3.363 2004-12-17T02:31:12.726180352 INFO 2025-06-26 06:12:15,940 calibrate.py _nudge_pos():1806 [1] 376: 0.080 -0.0023047 0.0002047 10210 34.03 -10.042 1.115 2004-12-17T03:06:00.723142912 INFO 2025-06-26 06:12:16,478 calibrate.py _nudge_pos():1806 [1] 433: 0.080 -0.0063370 -0.0036446 12740 42.46 -22.138 -15.904 2004-12-17T03:49:24.724756480 INFO 2025-06-26 06:12:16,959 calibrate.py _nudge_pos():1806 [1] 484: 0.080 -0.0033075 -0.0044809 10640 35.46 -13.841 -23.413 2004-12-17T04:25:42.725553280 INFO 2025-06-26 06:12:17,469 calibrate.py _nudge_pos():1806 [1] 537: 0.070 -0.0031403 -0.0033670 10540 35.13 -13.270 -17.760 2004-12-17T05:01:42.727582976 INFO 2025-06-26 06:12:18,105 calibrate.py _nudge_pos():1806 [1] 603: 0.080 -0.0012424 -0.0006540 3090 10.30 -17.914 -11.769 2004-12-17T05:13:05.720794624 INFO 2025-06-26 06:12:18,631 calibrate.py _nudge_pos():1806 [1] 658: 0.080 0.0004501 -0.0033337 11280 37.60 1.778 -16.430 2004-12-17T05:51:35.722548736 INFO 2025-06-26 06:12:19,207 calibrate.py _nudge_pos():1806 [1] 718: 0.090 0.0005720 -0.0013604 12280 40.93 2.076 -6.159 2004-12-17T06:33:30.720259712 INFO 2025-06-26 06:12:21,096 calibrate.py _nudge_pos():1862 [1] 888: - - - 4 0.01 - - INFO 2025-06-26 06:12:21,096 calibrate.py _nudge_pos():1868 [1] Points in final series = 95721 WARNING 2025-06-26 06:12:21,174 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 06:12:31,305 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:12:31,997 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:12:32,586 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:12:32,589 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.352.00/ctd1.nc INFO 2025-06-26 06:12:32,590 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 06:12:32,590 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 06:12:32,590 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 06:12:36,843 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 43 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:12:37,422 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 43 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:12:37,424 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.352.00/ctd2.nc WARNING 2025-06-26 06:12:37,426 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (509) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 06:12:37,426 calibrate.py _range_qc_combined_nc():898 [1] Setting 509 ctd2_salinity values to NaN INFO 2025-06-26 06:12:37,426 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 06:12:37,426 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 06:12:37,457 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 06:12:38,351 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [549780] INFO 2025-06-26 06:12:38,516 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 06:12:38,521 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 06:12:38,522 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.352.00 ERROR 2025-06-26 06:12:38,522 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.352.00 INFO 2025-06-26 06:12:38,599 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_cal.nc INFO 2025-06-26 06:12:41,060 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 06:12:41,064 process.py align():251 [1] Alignment steps for 2004.352.00 INFO 2025-06-26 06:12:41,093 align.py process_cal():139 [1] Processing dorado_2004.352.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.352.00 INFO 2025-06-26 06:12:41,123 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:12:41,126 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:12:41,199 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:12:41,203 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:12:41,270 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:12:41,274 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:12:41,315 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 06:12:41,316 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 06:12:41,343 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:12:41,347 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:12:41,412 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:12:41,417 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,477 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:12:41,481 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,542 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:12:41,547 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,606 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,610 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,670 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,674 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,734 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,739 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,799 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,803 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,864 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,868 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,928 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,933 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:41,994 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:41,998 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:42,058 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,062 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:42,122 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,127 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:42,186 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,190 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:12:42,251 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,256 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,316 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,320 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,379 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,384 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,444 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,448 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,508 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,513 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,572 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,576 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,635 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.352.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:12:42,639 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 06:12:42,704 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:12:42,751 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:12:42,796 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:12:42,842 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 06:12:42,889 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:12:42,938 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_align.nc INFO 2025-06-26 06:12:43,017 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 06:12:43,020 process.py resample():273 [1] Resampling steps for 2004.352.00 INFO 2025-06-26 06:12:43,020 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 06:12:43,047 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_align.nc mission netCDF file INFO 2025-06-26 06:12:43,053 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_align.nc mission netCDF file INFO 2025-06-26 06:12:43,054 resample.py get_mission_start_end():1145 [1] navigation: 2004-12-17T01:17:37.758626432 to 2004-12-17T06:36:42.527119872 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 06:12:43,056 resample.py get_mission_start_end():1145 [1] hs2 : 2004-12-17T01:17:20.629799808 to 2004-12-17T06:36:42.397128832 (0 days 00:00:00.189986944 before mission_end) INFO 2025-06-26 06:12:43,057 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-12-17T01:17:43.108259968 to 2004-12-17T06:36:42.417127424 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 06:12:43,059 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-12-17T01:18:00.497068672 to 2004-12-17T06:36:42.577116544 (0 days 00:00:00.009999232 before mission_end) INFO 2025-06-26 06:12:43,061 resample.py get_mission_start_end():1145 [1] isus : 2004-12-17T01:18:32.674864256 to 2004-12-17T06:36:42.097149312 (0 days 00:00:00.489966464 before mission_end) INFO 2025-06-26 06:12:43,062 resample.py get_mission_start_end():1145 [1] biolume : 2004-12-17T01:17:15.340128000 to 2004-12-17T06:36:41.697142656 (0 days 00:00:00.889973120 before mission_end) INFO 2025-06-26 06:12:43,064 resample.py get_mission_start_end():1145 [1] tailcone : 2004-12-17T01:17:16.430087552 to 2004-12-17T06:36:42.587115776 (0 days 00:00:00 before mission_end) INFO 2025-06-26 06:12:43,065 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_align.nc mission netCDF file INFO 2025-06-26 06:12:43,065 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,278 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,315 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,351 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,387 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,421 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,453 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,484 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,515 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,544 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,573 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,603 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,631 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,660 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,688 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,716 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,745 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,776 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,809 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,841 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,873 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,905 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,937 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,954 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,967 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,980 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:43,994 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:44,029 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 06:12:44,234 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_1S.nc INFO 2025-06-26 06:12:45,536 create_products.py gulper_odv():401 [1] No gulper times found for 2004.352.00 INFO 2025-06-26 06:12:45,536 process.py archive():337 [1] Archiving steps for 2004.352.00 INFO 2025-06-26 06:12:45,536 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00, BASE_PATH = /data/auv_data INFO 2025-06-26 06:12:45,536 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 06:12:45,538 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.352.00_1S.nc INFO 2025-06-26 06:12:45,561 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:12:45,561 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.352.00_cal.nc INFO 2025-06-26 06:12:45,645 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:12:45,646 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.352.00_align.nc INFO 2025-06-26 06:12:45,730 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:12:45,787 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,810 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,814 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,833 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,879 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,885 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,902 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,922 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,981 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004352/2004.352.00 done. INFO 2025-06-26 06:12:45,981 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 06:12:45,982 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.352.00/dorado_2004.352.00_processing.log /Volumes/AUVCTD/surveys/2004/netcdf