INFO 2025-06-26 12:45:31,575 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 12:45:31,575 process.py process_mission():434 [1] dorado_info[mission]["comment"] = BIOLUME mission - ctdToUse = ctd1 INFO 2025-06-26 12:45:31,575 process.py process_mission():449 [1] Processing BIOLUME mission 2007.144.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:45:31,575 process.py download_process():165 [1] Download and processing steps for 2007.144.02 INFO 2025-06-26 12:45:31,575 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007144/2007.144.02 INFO 2025-06-26 12:45:31,575 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007144/2007.144.02 to /data/auv_data/dorado/missionlogs/2007.144.02 INFO 2025-06-26 12:45:33,902 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.144.02 INFO 2025-06-26 12:45:33,903 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/ctdDriver.log (4161211 bytes) INFO 2025-06-26 12:45:34,190 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.144.02/ctdDriver.log: [ 8 150 224 244 325 393 448 540 754 1004 1026 1298 1328 1456 1468 1544 1592 1832 2165 2213 2235 2349 2391 2685 2743 3104 3235 3352 4185 4194 4368 4838 4948 4991 5023 5257 5327 5354 6305 6348 6438 7118 7363 7402 7519 7750 9468 9936 10741 10769 11267 11779 11901 12566 14822 14954 15483 15609 16170 16498 16590 16901 17839 19024 19122 21321 23216 23482 23706 24111 25315 26427 27097 27555 28866 28960 30828 31983 34130 37941 37967 38002 40122 43100 44579 47012] INFO 2025-06-26 12:45:34,201 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/ctdDriver2.log (4160941 bytes) INFO 2025-06-26 12:45:34,493 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.144.02/ctdDriver2.log: [ 146 228 237 318 386 441 533 743 748 997 1019 1291 1321 1449 1461 1538 1586 1826 2159 2206 2356 2677 2735 3097 3301 3524 4142 4178 4188 4208 4362 4832 4942 4985 5251 5298 5323 5350 6301 6344 6434 7115 7360 7399 7949 8037 10739 10767 11778 11901 11948 12062 12566 13767 14822 14954 15608 16169 16497 16589 17838 17866 19024 19122 19582 21320 22725 23215 23705 24110 26426 26797 27097 28960 30826 31981 37941 39954 40119 40187 43098 44576 47009] INFO 2025-06-26 12:45:34,507 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/gps.log (48524 bytes) INFO 2025-06-26 12:45:34,520 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/hydroscatlog.log (2841914 bytes) INFO 2025-06-26 12:45:34,849 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.144.02/hydroscatlog.log: [ 3 20 33 62 73 293 462 516 609 630 703 727 732 818 825 890 926 1096 1266 1365 1396 1523 1559 1851 2107 2236 2284 2436 2502 2563 2757 2815 2856 3177 3308 3380 3605 3628 3843 4223 4269 4444 5025 5100 5333 5379 5431 6425 6625 7197 7442 7443 7481 7599 7830 8032 8120 9536 9936 10821 11096 11983 11993 12031 12145 14903 15035 16251 16578 16670 16982 17918 19105 19203 19663 21400 22030 22804 23560 23785 24620 27622 27761 28945 29041 32060 33077 33856 34205 34686 37278 38016 38042 38077 40031 40197 43173 43443 43444 44652] INFO 2025-06-26 12:45:34,857 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/navigation.log (13913978 bytes) INFO 2025-06-26 12:45:35,859 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/isuslog.log (266645 bytes) INFO 2025-06-26 12:45:35,889 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/parosci.log (4967654 bytes) INFO 2025-06-26 12:45:36,332 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/tailCone.log (577483 bytes) INFO 2025-06-26 12:45:36,409 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.144.02/biolume.log (3227964 bytes) INFO 2025-06-26 12:45:36,711 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:45:36,889 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.99 seconds WARNING 2025-06-26 12:45:36,889 process.py download_process():196 [1] No lopc.bin file for 2007.144.02 INFO 2025-06-26 12:45:36,889 process.py calibrate():227 [1] Calibration steps for 2007.144.02 INFO 2025-06-26 12:45:37,013 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 12:45:37,015 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:45:37,830 calibrate.py _nudge_pos():1806 [1] 113: 0.180 0.0005998 -0.0004458 2388 8.05 11.067 -10.265 2007-05-24T19:25:41.925260800 INFO 2025-06-26 12:45:38,663 calibrate.py _nudge_pos():1806 [1] 200: 0.180 0.0018887 0.0002501 11276 37.76 7.425 1.227 2007-05-24T20:04:53.924137728 INFO 2025-06-26 12:45:39,493 calibrate.py _nudge_pos():1806 [1] 289: 0.180 0.0010483 0.0003930 8005 26.73 5.822 2.724 2007-05-24T20:33:05.928227584 INFO 2025-06-26 12:45:40,284 calibrate.py _nudge_pos():1806 [1] 372: 0.180 0.0017185 -0.0000024 10611 35.43 7.200 -0.012 2007-05-24T21:09:53.926969600 INFO 2025-06-26 12:45:41,074 calibrate.py _nudge_pos():1806 [1] 456: 0.170 -0.0000144 0.0000357 25 0.08 -26.690 82.734 2007-05-24T21:11:21.930940672 INFO 2025-06-26 12:45:41,094 calibrate.py _nudge_pos():1806 [1] 458: 0.180 0.0012015 -0.0003948 4587 15.31 11.646 -4.778 2007-05-24T21:26:41.927916544 INFO 2025-06-26 12:45:42,023 calibrate.py _nudge_pos():1806 [1] 554: 0.180 0.0023848 -0.0007801 11333 37.81 9.360 -3.823 2007-05-24T22:06:05.925971712 INFO 2025-06-26 12:45:42,836 calibrate.py _nudge_pos():1806 [1] 639: 0.180 0.0012599 0.0001023 7644 25.50 7.333 0.744 2007-05-24T22:32:59.925404928 INFO 2025-06-26 12:45:43,050 calibrate.py _nudge_pos():1862 [1] 628: - - - 2 0.00 - - INFO 2025-06-26 12:45:43,050 calibrate.py _nudge_pos():1868 [1] Points in final series = 58948 WARNING 2025-06-26 12:45:43,133 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 12:45:49,334 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:45:52,692 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:45:53,047 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:45:53,049 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.144.02/ctd1.nc INFO 2025-06-26 12:45:53,050 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:45:53,051 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 12:45:53,051 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:45:55,714 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:45:56,065 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:45:56,067 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.144.02/ctd2.nc INFO 2025-06-26 12:45:56,068 calibrate.py _range_qc_combined_nc():898 [1] Setting 157 ctd2_salinity values to NaN INFO 2025-06-26 12:45:56,068 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 12:45:56,068 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:45:56,090 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:45:56,594 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 707484 707485 707486] INFO 2025-06-26 12:45:56,700 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -6 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:45:56,706 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 12:45:56,706 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.144.02 ERROR 2025-06-26 12:45:56,706 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.144.02 INFO 2025-06-26 12:45:56,719 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_cal.nc INFO 2025-06-26 12:46:00,426 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 12:46:00,430 process.py align():251 [1] Alignment steps for 2007.144.02 INFO 2025-06-26 12:46:00,455 align.py process_cal():139 [1] Processing dorado_2007.144.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.144.02 INFO 2025-06-26 12:46:00,473 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:46:00,476 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:46:00,520 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:46:00,524 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:46:00,569 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:46:00,573 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:46:00,600 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:46:00,600 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:46:00,618 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:46:00,621 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:46:00,665 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,668 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,706 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,709 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,747 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,751 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,791 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,794 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,834 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,837 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,880 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,883 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,926 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,930 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:00,968 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:00,972 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,013 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,017 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,055 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,059 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,099 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,102 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,141 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,144 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,185 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,188 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,227 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,231 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,270 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,273 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,313 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,317 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,357 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,360 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,400 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,403 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,447 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,451 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,493 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.144.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:46:01,496 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:46:01,544 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:46:01,579 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:46:01,615 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:46:01,651 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:46:01,690 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 12:46:01,706 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_align.nc INFO 2025-06-26 12:46:01,768 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 12:46:01,770 process.py resample():273 [1] Resampling steps for 2007.144.02 INFO 2025-06-26 12:46:01,771 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:46:01,797 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_align.nc mission netCDF file INFO 2025-06-26 12:46:01,803 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_align.nc mission netCDF file INFO 2025-06-26 12:46:01,804 resample.py get_mission_start_end():1145 [1] navigation: 2007-05-24T19:16:21.033684480 to 2007-05-24T22:33:22.323870720 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:46:01,805 resample.py get_mission_start_end():1145 [1] hs2 : 2007-05-24T19:15:58.625219584 to 2007-05-24T22:33:22.273874176 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 12:46:01,807 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-05-24T19:16:15.524061952 to 2007-05-24T22:33:22.243876096 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 12:46:01,808 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-05-24T19:16:16.493995776 to 2007-05-24T22:33:22.193879552 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 12:46:01,809 resample.py get_mission_start_end():1145 [1] isus : 2007-05-24T19:17:02.540841216 to 2007-05-24T22:33:21.523925504 (0 days 00:00:00.799945216 before mission_end) INFO 2025-06-26 12:46:01,811 resample.py get_mission_start_end():1145 [1] biolume : 2007-05-24T19:15:46.676003840 to 2007-05-24T22:33:20.873935616 (0 days 00:00:01.449935104 before mission_end) INFO 2025-06-26 12:46:01,812 resample.py get_mission_start_end():1145 [1] tailcone : 2007-05-24T19:15:54.405508864 to 2007-05-24T22:33:21.973894912 (0 days 00:00:00.349975808 before mission_end) INFO 2025-06-26 12:46:01,812 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_align.nc mission netCDF file INFO 2025-06-26 12:46:01,813 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:01,952 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:01,978 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,010 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,038 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,061 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,085 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,108 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,130 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,151 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,171 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,193 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,214 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,235 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,257 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,287 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,318 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,344 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,366 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,389 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,411 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,433 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,454 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,466 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,478 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,489 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,501 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,514 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:46:02,672 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_1S.nc INFO 2025-06-26 12:46:04,751 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 12:46:14,326 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.144.02/dorado_2007.144.02_1S_Gulper.txt INFO 2025-06-26 12:46:14,326 process.py archive():337 [1] Archiving steps for 2007.144.02 INFO 2025-06-26 12:46:14,326 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02, BASE_PATH = /data/auv_data INFO 2025-06-26 12:46:14,327 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:46:14,328 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.144.02_1S.nc INFO 2025-06-26 12:46:14,341 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:46:14,342 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.144.02_cal.nc INFO 2025-06-26 12:46:14,389 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:46:14,390 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.144.02_align.nc INFO 2025-06-26 12:46:14,433 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:46:14,449 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,465 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,469 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,480 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,515 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,521 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,537 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,544 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,575 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007144/2007.144.02 done. INFO 2025-06-26 12:46:14,575 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:46:14,576 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.144.02_1S_Gulper.txt INFO 2025-06-26 12:46:14,581 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.144.02/dorado_2007.144.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 12:46:14,581 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.144.02/dorado_2007.144.02_processing.log /Volumes/AUVCTD/surveys/2007/netcdf