INFO 2025-06-26 11:06:01,060 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 11:06:01,060 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled by DMO 12/16/05 'Error in plot_survey_stats (line 139)' when reprocessing - ctdToUse = ctd1 INFO 2025-06-26 11:06:01,060 process.py process_mission():449 [1] Processing BIOLUME mission 2005.350.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:06:01,060 process.py download_process():165 [1] Download and processing steps for 2005.350.03 INFO 2025-06-26 11:06:01,060 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005350/2005.350.03 INFO 2025-06-26 11:06:01,060 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005350/2005.350.03 to /data/auv_data/dorado/missionlogs/2005.350.03 INFO 2025-06-26 11:06:04,587 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.350.03 INFO 2025-06-26 11:06:04,587 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/ctdDriver.log (9165067 bytes) INFO 2025-06-26 11:06:05,245 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.350.03/ctdDriver.log: [28203] INFO 2025-06-26 11:06:05,268 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/ctdDriver2.log (9164269 bytes) INFO 2025-06-26 11:06:05,907 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.350.03/ctdDriver2.log: [61914] INFO 2025-06-26 11:06:05,931 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/gps.log (72284 bytes) INFO 2025-06-26 11:06:05,947 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/hydroscatlog.log (6252374 bytes) INFO 2025-06-26 11:06:06,670 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.350.03/hydroscatlog.log: [24887 24888 24889 37328 37329 55982 55983] INFO 2025-06-26 11:06:06,685 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/navigation.log (30721426 bytes) INFO 2025-06-26 11:06:08,867 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/isuslog.log (525301 bytes) INFO 2025-06-26 11:06:08,922 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/parosci.log (13381910 bytes) INFO 2025-06-26 11:06:10,012 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.350.03/parosci.log: [ 20752 20754 21264 21266 21267 21269 21270 202789 246480 246481 246483 246484 246486] INFO 2025-06-26 11:06:10,046 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/tailCone.log (6255067 bytes) INFO 2025-06-26 11:06:10,803 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.350.03/biolume.log (7093356 bytes) INFO 2025-06-26 11:06:11,481 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:06:11,834 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.25 seconds WARNING 2025-06-26 11:06:11,835 process.py download_process():196 [1] No lopc.bin file for 2005.350.03 INFO 2025-06-26 11:06:11,835 process.py calibrate():227 [1] Calibration steps for 2005.350.03 INFO 2025-06-26 11:06:12,044 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 11:06:12,046 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:06:13,648 calibrate.py _nudge_pos():1806 [1] 184: 0.080 -0.0005958 0.0003910 1985 6.61 -13.346 10.955 2005-12-16T01:03:53.968511360 INFO 2025-06-26 11:06:14,517 calibrate.py _nudge_pos():1806 [1] 274: 0.070 -0.0033450 0.0016665 9994 33.31 -14.878 9.269 2005-12-16T01:38:41.975473152 INFO 2025-06-26 11:06:15,128 calibrate.py _nudge_pos():1806 [1] 337: 0.090 -0.0034156 0.0013960 10250 34.16 -14.820 7.572 2005-12-16T02:13:53.970791552 INFO 2025-06-26 11:06:15,798 calibrate.py _nudge_pos():1806 [1] 407: 0.110 -0.0037013 0.0010451 10095 33.65 -16.312 5.756 2005-12-16T02:48:41.967753856 INFO 2025-06-26 11:06:16,337 calibrate.py _nudge_pos():1806 [1] 462: 0.090 -0.0047707 0.0008558 10675 35.60 -19.880 4.455 2005-12-16T03:25:11.967728640 INFO 2025-06-26 11:06:16,918 calibrate.py _nudge_pos():1806 [1] 523: 0.100 -0.0066759 0.0011668 10677 35.60 -27.830 6.074 2005-12-16T04:01:47.967292288 INFO 2025-06-26 11:06:17,579 calibrate.py _nudge_pos():1806 [1] 590: 0.090 -0.0049323 0.0019485 10769 35.90 -20.396 10.058 2005-12-16T04:38:47.975211392 INFO 2025-06-26 11:06:18,081 calibrate.py _nudge_pos():1806 [1] 639: 0.100 -0.0000077 0.0000015 15 0.05 -24.399 6.140 2005-12-16T04:39:38.971717888 INFO 2025-06-26 11:06:18,091 calibrate.py _nudge_pos():1806 [1] 640: 0.100 -0.0014503 0.0004055 4479 14.95 -14.406 5.027 2005-12-16T04:54:35.970269440 INFO 2025-06-26 11:06:18,671 calibrate.py _nudge_pos():1806 [1] 699: 0.100 0.0001174 0.0004161 10863 36.23 0.481 2.128 2005-12-16T05:31:47.967367168 INFO 2025-06-26 11:06:19,222 calibrate.py _nudge_pos():1806 [1] 755: 0.100 -0.0002655 -0.0000634 10765 35.88 -1.099 -0.327 2005-12-16T06:08:35.976108032 INFO 2025-06-26 11:06:19,778 calibrate.py _nudge_pos():1806 [1] 811: 0.110 0.0000236 0.0000280 11870 39.58 0.089 0.131 2005-12-16T06:49:05.969642112 INFO 2025-06-26 11:06:20,314 calibrate.py _nudge_pos():1806 [1] 860: 0.100 0.0003965 -0.0003501 10468 34.90 1.689 -1.859 2005-12-16T07:24:47.972904960 INFO 2025-06-26 11:06:20,898 calibrate.py _nudge_pos():1806 [1] 918: 0.120 0.0004254 -0.0003531 9969 33.25 1.903 -1.968 2005-12-16T07:58:59.972333184 INFO 2025-06-26 11:06:21,429 calibrate.py _nudge_pos():1806 [1] 971: 0.110 -0.0000496 -0.0000090 2524 8.43 -0.876 -0.197 2005-12-16T08:08:17.974107520 INFO 2025-06-26 11:06:21,640 calibrate.py _nudge_pos():1862 [1] 970: - - - 3 0.01 - - INFO 2025-06-26 11:06:21,640 calibrate.py _nudge_pos():1868 [1] Points in final series = 130166 WARNING 2025-06-26 11:06:26,238 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:06:40,079 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:06:47,472 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:06:48,261 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:06:48,264 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.350.03/ctd1.nc INFO 2025-06-26 11:06:48,265 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 11:06:48,265 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 11:06:48,266 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:06:54,054 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:06:54,838 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:06:54,840 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.350.03/ctd2.nc INFO 2025-06-26 11:06:54,842 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 11:06:54,842 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 11:06:54,842 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:06:54,880 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:06:56,078 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 600 80100 84900 102300 196620 1279980 1555800 1555801 1555802 1555803 1555804 1555805 1555806 1555807 1555808 1555809 1555810 1555811 1555812 1555813 1555814 1555815 1555816] INFO 2025-06-26 11:06:56,316 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:06:56,321 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 11:06:56,322 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.350.03 ERROR 2025-06-26 11:06:56,322 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.350.03 INFO 2025-06-26 11:06:56,423 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_cal.nc INFO 2025-06-26 11:07:04,522 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 11:07:04,526 process.py align():251 [1] Alignment steps for 2005.350.03 INFO 2025-06-26 11:07:04,556 align.py process_cal():139 [1] Processing dorado_2005.350.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.350.03 INFO 2025-06-26 11:07:04,593 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:07:04,597 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:07:04,691 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:07:04,697 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:07:04,787 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:07:04,792 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:07:04,847 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:07:04,847 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:07:04,883 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:07:04,888 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:07:04,979 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:07:04,984 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,064 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:07:05,068 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,146 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:07:05,151 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,229 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,233 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,312 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,317 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,395 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,400 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,478 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,483 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,560 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,565 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,643 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,647 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,725 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,731 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,809 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,814 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,892 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,897 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:05,974 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:05,978 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,058 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,063 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,141 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,146 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,222 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,228 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,306 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,311 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,388 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,393 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,472 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,477 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,556 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.350.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:07:06,561 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:07:06,662 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:07:06,729 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:07:06,796 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.63 INFO 2025-06-26 11:07:06,866 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:07:06,938 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:07:07,000 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_align.nc INFO 2025-06-26 11:07:07,091 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 11:07:07,093 process.py resample():273 [1] Resampling steps for 2005.350.03 INFO 2025-06-26 11:07:07,094 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:07:07,122 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_align.nc mission netCDF file INFO 2025-06-26 11:07:07,128 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_align.nc mission netCDF file INFO 2025-06-26 11:07:07,130 resample.py get_mission_start_end():1145 [1] navigation: 2005-12-16T00:54:35.986735872 to 2005-12-16T08:08:38.572696448 (0 days 00:00:00.079994496 before mission_end) INFO 2025-06-26 11:07:07,132 resample.py get_mission_start_end():1145 [1] hs2 : 2005-12-16T00:54:19.207885312 to 2005-12-16T08:08:38.592695040 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 11:07:07,133 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-12-16T00:54:41.706343936 to 2005-12-16T08:08:38.602694272 (0 days 00:00:00.049996672 before mission_end) INFO 2025-06-26 11:07:07,135 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-12-16T00:54:41.726342656 to 2005-12-16T08:08:38.612693760 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 11:07:07,137 resample.py get_mission_start_end():1145 [1] isus : 2005-12-16T00:55:43.522109312 to 2005-12-16T08:08:37.842746496 (0 days 00:00:00.809944448 before mission_end) INFO 2025-06-26 11:07:07,138 resample.py get_mission_start_end():1145 [1] biolume : 2005-12-16T00:54:13.428246912 to 2005-12-16T08:08:37.662724480 (0 days 00:00:00.989966464 before mission_end) INFO 2025-06-26 11:07:07,140 resample.py get_mission_start_end():1145 [1] tailcone : 2005-12-16T00:54:13.848252288 to 2005-12-16T08:08:38.652690944 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:07:07,141 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_align.nc mission netCDF file INFO 2025-06-26 11:07:07,141 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,421 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,470 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,518 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,564 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,605 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,645 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,685 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,724 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,762 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,799 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,836 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,873 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,909 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,945 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:07,981 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,020 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,060 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,101 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,140 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,189 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,233 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,271 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,289 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,305 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,319 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,337 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,381 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:07:08,639 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_1S.nc INFO 2025-06-26 11:07:09,961 create_products.py gulper_odv():401 [1] No gulper times found for 2005.350.03 INFO 2025-06-26 11:07:09,962 process.py archive():337 [1] Archiving steps for 2005.350.03 INFO 2025-06-26 11:07:09,962 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03, BASE_PATH = /data/auv_data INFO 2025-06-26 11:07:09,963 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 11:07:09,964 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.350.03_1S.nc INFO 2025-06-26 11:07:09,990 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 11:07:09,991 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.350.03_cal.nc INFO 2025-06-26 11:07:10,106 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 11:07:10,107 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.350.03_align.nc INFO 2025-06-26 11:07:10,215 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 11:07:10,244 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,270 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,277 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,298 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,390 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,397 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,434 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,458 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,532 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005350/2005.350.03 done. INFO 2025-06-26 11:07:10,533 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:07:10,533 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.350.03/dorado_2005.350.03_processing.log /Volumes/AUVCTD/surveys/2005/netcdf