INFO 2025-06-26 10:50:38,988 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 10:50:38,988 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Conducted from the Sproul on John Ryan's LOCO project - ctdToUse = ctd1 INFO 2025-06-26 10:50:38,988 process.py process_mission():449 [1] Processing LOCO mission 2005.240.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:50:38,988 process.py download_process():165 [1] Download and processing steps for 2005.240.00 INFO 2025-06-26 10:50:38,989 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005240/2005.240.00 INFO 2025-06-26 10:50:38,989 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005240/2005.240.00 to /data/auv_data/dorado/missionlogs/2005.240.00 INFO 2025-06-26 10:50:42,509 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.240.00 INFO 2025-06-26 10:50:42,510 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/ctdDriver.log (8119539 bytes) INFO 2025-06-26 10:50:43,120 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/ctdDriver2.log (8119621 bytes) INFO 2025-06-26 10:50:43,719 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/gps.log (119948 bytes) INFO 2025-06-26 10:50:43,741 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/hydroscatlog.log (5539334 bytes) INFO 2025-06-26 10:50:44,399 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/navigation.log (27224378 bytes) INFO 2025-06-26 10:50:46,362 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/isuslog.log (495349 bytes) INFO 2025-06-26 10:50:46,415 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/parosci.log (11850422 bytes) INFO 2025-06-26 10:50:47,374 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.240.00/parosci.log: [182559] INFO 2025-06-26 10:50:47,406 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/tailCone.log (5542171 bytes) INFO 2025-06-26 10:50:48,082 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.240.00/biolume.log (6284428 bytes) INFO 2025-06-26 10:50:48,672 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:50:49,008 logs2netcdfs.py download_process_logs():807 [1] Time to process: 6.50 seconds WARNING 2025-06-26 10:50:49,009 process.py download_process():196 [1] No lopc.bin file for 2005.240.00 INFO 2025-06-26 10:50:49,009 process.py calibrate():227 [1] Calibration steps for 2005.240.00 INFO 2025-06-26 10:50:49,205 calibrate.py _navigation_process():1637 [1] Removing points outside of Monterey Bay for 2005.240.00/navigation.nc INFO 2025-06-26 10:50:49,207 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('navigation_latitude', Range(min=36, max=37)), ('navigation_longitude', Range(min=-122.1, max=-121.7))] INFO 2025-06-26 10:50:49,208 calibrate.py _range_qc_combined_nc():916 [1] navigation_time: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,214 calibrate.py _range_qc_combined_nc():916 [1] navigation_roll: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,216 calibrate.py _range_qc_combined_nc():916 [1] navigation_pitch: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,218 calibrate.py _range_qc_combined_nc():916 [1] navigation_yaw: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,221 calibrate.py _range_qc_combined_nc():916 [1] navigation_posx: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,223 calibrate.py _range_qc_combined_nc():916 [1] navigation_posy: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,225 calibrate.py _range_qc_combined_nc():916 [1] navigation_depth: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,228 calibrate.py _range_qc_combined_nc():916 [1] navigation_mWaterSpeed: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,230 calibrate.py _range_qc_combined_nc():916 [1] navigation_latitude: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,233 calibrate.py _range_qc_combined_nc():916 [1] navigation_longitude: deleting 0 values found outside of above ranges: [] INFO 2025-06-26 10:50:49,241 calibrate.py _range_qc_combined_nc():936 [1] Done range checking navigation INFO 2025-06-26 10:50:49,245 calibrate.py _gps_process():2069 [1] Removing points outside of Monterey Bay for 2005.240.00/gps.nc INFO 2025-06-26 10:50:49,247 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('gps_latitude', Range(min=36, max=37)), ('gps_longitude', Range(min=-122.1, max=-121.7))] INFO 2025-06-26 10:50:49,247 calibrate.py _range_qc_combined_nc():916 [1] gps_time: deleting 35 values found outside of above ranges: ['2005-08-28T04:01:42.231508480' '2005-08-28T04:01:43.241439360' '2005-08-28T04:01:44.251370240' '2005-08-28T04:01:45.261300992' '2005-08-28T04:01:46.241233792' '2005-08-28T04:01:47.241165440' '2005-08-28T04:02:33.228015232' '2005-08-28T04:03:07.235685376' '2005-08-28T04:03:21.234726400' '2005-08-28T04:03:22.234658048' '2005-08-28T04:03:23.224590080' '2005-08-28T04:03:26.244383360' '2005-08-28T04:03:27.234315392' '2005-08-28T04:03:28.234246912' '2005-08-28T04:03:29.244177792' '2005-08-28T04:03:32.243972352' '2005-08-28T04:03:33.233904384' '2005-08-28T04:03:34.243835264' '2005-08-28T04:03:35.233767552' '2005-08-28T04:03:38.243561216' '2005-08-28T04:03:39.233493376' '2005-08-28T04:03:40.233424896' '2005-08-28T04:03:41.243355776' '2005-08-28T04:03:44.243150208' '2005-08-28T04:03:45.233082496' '2005-08-28T04:03:46.233013888' '2005-08-28T04:03:47.242944768' '2005-08-28T04:03:50.242739200' '2005-08-28T04:03:51.272668544' '2005-08-28T04:03:52.242602368' '2005-08-28T04:03:53.242533632' '2005-08-28T04:03:56.242328192' '2005-08-28T04:03:57.232260480' '2005-08-28T04:03:58.232192000' '2005-08-28T04:03:59.232123392'] INFO 2025-06-26 10:50:49,250 calibrate.py _range_qc_combined_nc():916 [1] gps_latitude: deleting 35 values found outside of above ranges: [11.45307833 11.48237117 11.511627 11.54092117 11.57020733 11.59951467 12.957433 13.97284633 14.393604 14.42371783 14.45383133 14.5442215 14.57437583 14.60453883 14.63470317 14.72522117 14.7554055 14.78559217 14.81579883 14.90646617 14.93669367 14.96693067 14.997178 15.08796433 15.11823167 15.14850567 15.17879983 15.26968683 15.30001083 15.33033567 15.3606625 15.4516795 15.48202233 15.5123785 15.54274767] INFO 2025-06-26 10:50:49,252 calibrate.py _range_qc_combined_nc():916 [1] gps_longitude: deleting 35 values found outside of above ranges: [-88.376611 -88.41028117 -88.443915 -88.47758417 -88.51124267 -88.5449185 -90.10097317 -91.26085583 -91.7410755 -91.77543917 -91.809807 -91.91296817 -91.94737967 -91.9818005 -92.01622117 -92.11953117 -92.15398 -92.18843433 -92.22291117 -92.32639517 -92.36089917 -92.39541267 -92.42994 -92.533574 -92.56812633 -92.60269283 -92.63727467 -92.74105467 -92.77567817 -92.810303 -92.84493533 -92.94887967 -92.98353833 -93.01821433 -93.052905 ] INFO 2025-06-26 10:50:49,255 calibrate.py _range_qc_combined_nc():936 [1] Done range checking gps INFO 2025-06-26 10:50:49,255 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 10:50:49,257 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:50:49,994 calibrate.py _nudge_pos():1806 [1] 92: 0.150 0.0004143 -0.0011487 8370 27.90 2.200 -7.630 2005-08-28T02:07:54.079269120 INFO 2025-06-26 10:50:50,953 calibrate.py _nudge_pos():1806 [1] 192: 0.150 -0.0003906 0.0002275 7695 25.65 -2.257 1.643 2005-08-28T02:35:12.087057792 INFO 2025-06-26 10:50:51,930 calibrate.py _nudge_pos():1806 [1] 289: 0.140 -0.0002932 0.0000474 8315 27.71 -1.568 0.317 2005-08-28T03:04:31.086558080 INFO 2025-06-26 10:50:52,769 calibrate.py _nudge_pos():1806 [1] 376: 0.140 -0.0003067 -0.0000201 8175 27.25 -1.669 -0.137 2005-08-28T03:33:12.088661376 INFO 2025-06-26 10:50:53,682 calibrate.py _nudge_pos():1806 [1] 470: 0.140 -0.0003666 -0.0000725 8775 29.25 -1.859 -0.459 2005-08-28T04:04:00.082065152 INFO 2025-06-26 10:50:54,567 calibrate.py _nudge_pos():1806 [1] 560: 0.150 -0.0006892 0.0003138 9845 32.81 -3.117 1.772 2005-08-28T04:38:18.081082624 INFO 2025-06-26 10:50:55,372 calibrate.py _nudge_pos():1806 [1] 643: 0.150 -0.0012940 0.0008414 8140 27.13 -7.075 5.747 2005-08-28T05:06:48.083939328 INFO 2025-06-26 10:50:56,257 calibrate.py _nudge_pos():1806 [1] 734: 0.150 -0.0015406 0.0003525 8130 27.10 -8.432 2.411 2005-08-28T05:35:24.086385280 INFO 2025-06-26 10:50:57,056 calibrate.py _nudge_pos():1806 [1] 815: 0.150 -0.0013897 0.0003638 7610 25.36 -8.123 2.658 2005-08-28T06:02:06.086640640 INFO 2025-06-26 10:50:57,922 calibrate.py _nudge_pos():1806 [1] 903: 0.150 -0.0010008 0.0002438 5625 18.75 -7.913 2.410 2005-08-28T06:22:18.083613184 INFO 2025-06-26 10:50:58,794 calibrate.py _nudge_pos():1806 [1] 991: 0.150 -0.0020563 -0.0017864 6765 22.55 -13.516 -14.682 2005-08-28T06:46:18.084966400 INFO 2025-06-26 10:50:59,633 calibrate.py _nudge_pos():1806 [1] 1075: 0.150 -0.0023312 -0.0019542 7565 25.21 -13.699 -14.362 2005-08-28T07:12:54.085632768 INFO 2025-06-26 10:51:00,472 calibrate.py _nudge_pos():1806 [1] 1158: 0.160 -0.0024155 -0.0020189 7930 26.43 -13.538 -14.155 2005-08-28T07:40:42.081367296 INFO 2025-06-26 10:51:01,327 calibrate.py _nudge_pos():1806 [1] 1244: 0.160 -0.0014754 -0.0010077 4495 14.98 -14.587 -12.466 2005-08-28T07:57:06.083958400 INFO 2025-06-26 10:51:05,096 calibrate.py _nudge_pos():1862 [1] 1598: - - - 2 0.00 - - INFO 2025-06-26 10:51:05,096 calibrate.py _nudge_pos():1868 [1] Points in final series = 115348 WARNING 2025-06-26 10:51:09,087 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:51:09,320 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 92307 INFO 2025-06-26 10:51:10,045 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:51:10,972 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:51:11,694 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:51:11,696 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.240.00/ctd1.nc INFO 2025-06-26 10:51:11,698 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 10:51:11,698 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 10:51:11,698 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:51:12,538 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:51:13,247 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 10:51:13,250 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.240.00/ctd2.nc INFO 2025-06-26 10:51:13,251 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:51:13,252 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 10:51:13,252 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:51:13,288 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:51:14,348 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 524100 1112340 1112341 1112342] INFO 2025-06-26 10:51:14,571 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:51:14,577 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 10:51:14,577 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.240.00 ERROR 2025-06-26 10:51:14,577 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.240.00 INFO 2025-06-26 10:51:14,667 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_cal.nc INFO 2025-06-26 10:51:14,769 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 10:51:14,775 process.py align():251 [1] Alignment steps for 2005.240.00 INFO 2025-06-26 10:51:14,805 align.py process_cal():139 [1] Processing dorado_2005.240.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.240.00 INFO 2025-06-26 10:51:14,838 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:51:14,842 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:51:14,926 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:51:14,931 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:51:15,012 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:51:15,018 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:51:15,067 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:51:15,067 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:51:15,099 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:51:15,105 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:51:15,183 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:51:15,188 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,259 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:51:15,263 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,336 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:51:15,340 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,419 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,424 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,496 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,501 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,570 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,575 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,645 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,649 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,719 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,723 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,808 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,813 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,883 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,888 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:15,958 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:15,963 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,033 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,037 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,107 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,111 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,182 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,186 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,258 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,262 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,335 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,340 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,412 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,417 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,488 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,493 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,563 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,567 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,638 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.240.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:51:16,642 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:51:16,730 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:51:16,795 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:51:16,857 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.67 INFO 2025-06-26 10:51:16,921 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:51:16,988 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:51:17,045 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_align.nc INFO 2025-06-26 10:51:17,131 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 10:51:17,134 process.py resample():273 [1] Resampling steps for 2005.240.00 INFO 2025-06-26 10:51:17,134 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:51:17,161 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_align.nc mission netCDF file INFO 2025-06-26 10:51:17,167 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_align.nc mission netCDF file INFO 2025-06-26 10:51:17,169 resample.py get_mission_start_end():1145 [1] navigation: 2005-08-28T01:38:50.898685184 to 2005-08-28T08:03:20.488310144 (0 days 00:00:00.169988096 before mission_end) INFO 2025-06-26 10:51:17,171 resample.py get_mission_start_end():1145 [1] hs2 : 2005-08-28T01:38:33.539874304 to 2005-08-28T08:03:20.608301824 (0 days 00:00:00.049996416 before mission_end) INFO 2025-06-26 10:51:17,172 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-08-28T01:38:56.208321280 to 2005-08-28T08:03:20.638299648 (0 days 00:00:00.019998592 before mission_end) INFO 2025-06-26 10:51:17,174 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-08-28T01:38:56.228320128 to 2005-08-28T08:03:20.658298240 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:51:17,176 resample.py get_mission_start_end():1145 [1] isus : 2005-08-28T01:39:56.954160000 to 2005-08-28T08:03:20.568304512 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 10:51:17,177 resample.py get_mission_start_end():1145 [1] biolume : 2005-08-28T01:38:28.720170240 to 2005-08-28T08:03:19.268359424 (0 days 00:00:01.389938816 before mission_end) INFO 2025-06-26 10:51:17,179 resample.py get_mission_start_end():1145 [1] tailcone : 2005-08-28T01:38:29.070180480 to 2005-08-28T08:03:20.658298240 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:51:17,179 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_align.nc mission netCDF file INFO 2025-06-26 10:51:17,180 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,447 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,492 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,536 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,578 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,616 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,653 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,691 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,727 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,761 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,795 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,829 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,863 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,897 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,931 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:17,967 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,001 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,039 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,074 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,110 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,146 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,183 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,220 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,238 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,253 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,267 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,284 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,327 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:51:18,564 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_1S.nc INFO 2025-06-26 10:51:20,245 create_products.py gulper_odv():401 [1] No gulper times found for 2005.240.00 INFO 2025-06-26 10:51:20,246 process.py archive():337 [1] Archiving steps for 2005.240.00 INFO 2025-06-26 10:51:20,246 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00, BASE_PATH = /data/auv_data INFO 2025-06-26 10:51:20,246 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:51:20,248 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.240.00_1S.nc INFO 2025-06-26 10:51:20,269 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:51:20,270 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.240.00_cal.nc INFO 2025-06-26 10:51:20,379 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:51:20,380 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.240.00_align.nc INFO 2025-06-26 10:51:20,476 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:51:20,504 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,531 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,556 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,636 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,643 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,679 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,701 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,765 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005240/2005.240.00 done. INFO 2025-06-26 10:51:20,765 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:51:20,765 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.240.00/dorado_2005.240.00_processing.log /Volumes/AUVCTD/surveys/2005/netcdf