INFO 2025-06-26 10:38:55,640 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 10:38:55,641 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ctdToUse = ctd1 INFO 2025-06-26 10:38:55,641 process.py process_mission():449 [1] Processing BIOLUME mission 2005.140.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 10:38:55,641 process.py download_process():165 [1] Download and processing steps for 2005.140.00 INFO 2025-06-26 10:38:55,641 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005140/2005.140.00 INFO 2025-06-26 10:38:55,641 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005140/2005.140.00 to /data/auv_data/dorado/missionlogs/2005.140.00 INFO 2025-06-26 10:38:56,367 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.140.00 INFO 2025-06-26 10:38:56,368 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/ctdDriver.log (8845187 bytes) INFO 2025-06-26 10:38:57,015 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/ctdDriver2.log (8845445 bytes) INFO 2025-06-26 10:38:57,698 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/gps.log (77252 bytes) INFO 2025-06-26 10:38:57,715 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/hydroscatlog.log (6034574 bytes) INFO 2025-06-26 10:38:58,500 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.140.00/hydroscatlog.log: [66360 81428 81430] INFO 2025-06-26 10:38:58,515 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/navigation.log (29656122 bytes) INFO 2025-06-26 10:39:00,656 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/isuslog.log (543413 bytes) INFO 2025-06-26 10:39:00,712 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.140.00/isuslog.log: [1 3 4 5 6 7] INFO 2025-06-26 10:39:00,714 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/parosci.log (12909206 bytes) INFO 2025-06-26 10:39:01,770 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2005.140.00/parosci.log: [ 23953 23954 35922 53861 177467 177470 177472] INFO 2025-06-26 10:39:01,804 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/tailCone.log (6037339 bytes) INFO 2025-06-26 10:39:02,570 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.140.00/biolume.log (6846108 bytes) INFO 2025-06-26 10:39:03,239 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 10:39:03,593 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.22 seconds WARNING 2025-06-26 10:39:03,593 process.py download_process():196 [1] No lopc.bin file for 2005.140.00 INFO 2025-06-26 10:39:03,593 process.py calibrate():227 [1] Calibration steps for 2005.140.00 INFO 2025-06-26 10:39:03,801 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 10:39:03,803 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 10:39:05,329 calibrate.py _nudge_pos():1806 [1] 172: 0.130 -0.0000716 -0.0000467 1493 4.98 -2.130 -1.736 2005-05-20T03:42:36.159014400 INFO 2025-06-26 10:39:06,386 calibrate.py _nudge_pos():1806 [1] 281: 0.130 -0.0008627 0.0003898 9749 32.50 -3.933 2.222 2005-05-20T04:16:54.158032000 INFO 2025-06-26 10:39:07,006 calibrate.py _nudge_pos():1806 [1] 343: 0.130 -0.0007660 0.0003666 10150 33.83 -3.356 2.008 2005-05-20T04:51:45.154788736 INFO 2025-06-26 10:39:07,618 calibrate.py _nudge_pos():1806 [1] 404: 0.150 -0.0013427 0.0000954 10665 35.55 -5.601 0.497 2005-05-20T05:28:18.154557952 INFO 2025-06-26 10:39:08,179 calibrate.py _nudge_pos():1806 [1] 462: 0.140 0.0000040 -0.0000039 15 0.05 12.693 -15.342 2005-05-20T05:29:18.150448128 INFO 2025-06-26 10:39:08,199 calibrate.py _nudge_pos():1806 [1] 464: 0.150 -0.0022121 -0.0004994 9895 32.98 -9.950 -2.806 2005-05-20T06:02:18.154808576 INFO 2025-06-26 10:39:08,811 calibrate.py _nudge_pos():1806 [1] 527: 0.140 -0.0016657 -0.0004571 9585 31.96 -7.733 -2.650 2005-05-20T06:35:18.159168896 INFO 2025-06-26 10:39:09,396 calibrate.py _nudge_pos():1806 [1] 587: 0.140 -0.0016927 0.0002050 10328 34.43 -7.298 1.103 2005-05-20T07:10:43.153596928 INFO 2025-06-26 10:39:09,924 calibrate.py _nudge_pos():1806 [1] 640: 0.130 -0.0000063 -0.0000098 20 0.06 -14.673 -28.745 2005-05-20T07:11:39.159760000 INFO 2025-06-26 10:39:09,974 calibrate.py _nudge_pos():1806 [1] 645: 0.130 -0.0007329 0.0003147 4705 15.68 -6.939 3.719 2005-05-20T07:27:24.155023616 INFO 2025-06-26 10:39:10,556 calibrate.py _nudge_pos():1806 [1] 704: 0.130 0.0009965 -0.0002878 9758 32.53 4.549 -1.639 2005-05-20T08:00:54.157328896 INFO 2025-06-26 10:39:11,174 calibrate.py _nudge_pos():1806 [1] 767: 0.130 0.0010560 -0.0003184 9348 31.16 5.034 -1.893 2005-05-20T08:33:06.154978048 INFO 2025-06-26 10:39:11,891 calibrate.py _nudge_pos():1806 [1] 839: 0.130 0.0007706 0.0001644 9664 32.21 3.555 0.946 2005-05-20T09:06:30.157694336 INFO 2025-06-26 10:39:12,420 calibrate.py _nudge_pos():1806 [1] 892: 0.130 0.0006879 0.0003530 9910 33.03 3.096 1.980 2005-05-20T09:40:24.158355712 INFO 2025-06-26 10:39:12,957 calibrate.py _nudge_pos():1806 [1] 946: 0.140 0.0006762 0.0005618 9814 32.71 3.074 3.182 2005-05-20T10:14:00.150250880 INFO 2025-06-26 10:39:13,434 calibrate.py _nudge_pos():1806 [1] 993: 0.130 0.0001584 0.0000983 2440 8.13 2.896 2.240 2005-05-20T10:22:54.153669120 INFO 2025-06-26 10:39:13,938 calibrate.py _nudge_pos():1806 [1] 1043: 0.150 0.0002133 0.0001350 2995 9.98 3.179 2.507 2005-05-20T10:33:43.159209216 INFO 2025-06-26 10:39:14,122 calibrate.py _nudge_pos():1862 [1] 1039: - - - 4 0.01 - - INFO 2025-06-26 10:39:14,122 calibrate.py _nudge_pos():1868 [1] Points in final series = 125652 WARNING 2025-06-26 10:39:18,492 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 10:39:31,076 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 100558 INFO 2025-06-26 10:39:31,852 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:39:32,815 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:39:33,577 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:39:33,580 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.140.00/ctd1.nc INFO 2025-06-26 10:39:33,581 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 10:39:33,582 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 10:39:33,582 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 10:39:34,486 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:39:35,246 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 10:39:35,248 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.140.00/ctd2.nc INFO 2025-06-26 10:39:35,250 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 10:39:35,250 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 10:39:35,250 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 10:39:36,078 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 10:39:37,237 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 29580 29760 30000 30360 34680 35040 35220 35580 35760 78960 79320 79920 82020 82200 82380 194640 212460 223860 252360 260760 261960 369300 372600 536880 555540 567840 568020 754320 756420 758940 759300 778320 778321 778322 816060 819540 930000 931620 946860 1018860 1093140 1145220 1205160 1205340 1208100 1268760 1269540 1270980 1380060 1492620 1492800] INFO 2025-06-26 10:39:37,471 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 10:39:37,477 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 10:39:37,478 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.140.00 ERROR 2025-06-26 10:39:37,478 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.140.00 INFO 2025-06-26 10:39:37,648 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_cal.nc INFO 2025-06-26 10:39:37,756 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 10:39:37,760 process.py align():251 [1] Alignment steps for 2005.140.00 INFO 2025-06-26 10:39:37,791 align.py process_cal():139 [1] Processing dorado_2005.140.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.140.00 INFO 2025-06-26 10:39:37,828 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:39:37,833 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:39:37,922 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:39:37,928 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:39:38,017 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:39:38,023 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:39:38,078 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 10:39:38,078 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 10:39:38,114 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 10:39:38,119 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:39:38,205 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:39:38,211 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,287 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:39:38,292 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,370 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 10:39:38,375 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,455 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,460 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,540 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,546 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,623 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,628 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,704 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,709 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,784 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,789 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,866 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,871 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:38,948 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:38,953 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,031 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,037 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,130 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,135 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,211 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,216 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,293 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,298 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,376 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,381 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,461 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,467 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,545 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,550 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,630 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,635 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,714 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,719 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,797 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.140.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 10:39:39,802 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 10:39:39,901 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:39:39,969 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:39:40,043 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 10:39:40,118 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 10:39:40,192 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 10:39:40,254 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_align.nc INFO 2025-06-26 10:39:40,344 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 10:39:40,346 process.py resample():273 [1] Resampling steps for 2005.140.00 INFO 2025-06-26 10:39:40,347 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 10:39:40,373 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_align.nc mission netCDF file INFO 2025-06-26 10:39:40,380 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_align.nc mission netCDF file INFO 2025-06-26 10:39:40,382 resample.py get_mission_start_end():1145 [1] navigation: 2005-05-20T03:35:07.159773056 to 2005-05-20T10:34:00.957989888 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:39:40,384 resample.py get_mission_start_end():1145 [1] hs2 : 2005-05-20T03:34:50.110940928 to 2005-05-20T10:34:00.947990656 (0 days 00:00:00.009999232 before mission_end) INFO 2025-06-26 10:39:40,386 resample.py get_mission_start_end():1145 [1] ctd1 : 2005-05-20T03:35:12.579401728 to 2005-05-20T10:34:00.957989888 (0 days 00:00:00 before mission_end) INFO 2025-06-26 10:39:40,388 resample.py get_mission_start_end():1145 [1] ctd2 : 2005-05-20T03:35:12.699393536 to 2005-05-20T10:34:00.847997440 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 10:39:40,390 resample.py get_mission_start_end():1145 [1] isus : 2005-05-20T03:35:46.527076224 to 2005-05-20T10:34:00.937991424 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 10:39:40,392 resample.py get_mission_start_end():1145 [1] biolume : 2005-05-20T03:34:45.011255936 to 2005-05-20T10:34:00.018020096 (0 days 00:00:00.939969792 before mission_end) INFO 2025-06-26 10:39:40,394 resample.py get_mission_start_end():1145 [1] tailcone : 2005-05-20T03:34:45.121282816 to 2005-05-20T10:34:00.847997440 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 10:39:40,395 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_align.nc mission netCDF file INFO 2025-06-26 10:39:40,395 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,677 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,723 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,769 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,814 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,856 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,896 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,935 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:40,975 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,012 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,050 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,087 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,142 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,178 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,214 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,250 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,286 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,324 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,362 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,399 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,437 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,474 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,512 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,530 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,546 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,561 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,578 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,622 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 10:39:41,861 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_1S.nc INFO 2025-06-26 10:39:42,946 create_products.py gulper_odv():401 [1] No gulper times found for 2005.140.00 INFO 2025-06-26 10:39:42,947 process.py archive():337 [1] Archiving steps for 2005.140.00 INFO 2025-06-26 10:39:42,947 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00, BASE_PATH = /data/auv_data INFO 2025-06-26 10:39:42,948 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00 files to /Volumes/AUVCTD/surveys/2005/netcdf INFO 2025-06-26 10:39:42,949 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.140.00_1S.nc INFO 2025-06-26 10:39:42,974 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:39:42,975 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.140.00_cal.nc INFO 2025-06-26 10:39:43,103 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:39:43,104 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.140.00_align.nc INFO 2025-06-26 10:39:43,206 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done. INFO 2025-06-26 10:39:43,234 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,262 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,267 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,288 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,381 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,388 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,425 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,450 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005140/2005.140.00 done. INFO 2025-06-26 10:39:43,524 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 10:39:43,524 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.140.00/dorado_2005.140.00_processing.log /Volumes/AUVCTD/surveys/2005/netcdf