INFO 2025-06-26 13:44:51,790 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 13:44:51,790 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Kanna control tests south of M0 - ctdToUse = ctd1 INFO 2025-06-26 13:44:51,790 process.py process_mission():449 [1] Processing AUVCTD mission 2007.325.16 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:44:51,790 process.py download_process():165 [1] Download and processing steps for 2007.325.16 INFO 2025-06-26 13:44:51,791 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007325/2007.325.16 INFO 2025-06-26 13:44:51,791 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007325/2007.325.16 to /data/auv_data/dorado/missionlogs/2007.325.16 INFO 2025-06-26 13:44:53,142 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.325.16 INFO 2025-06-26 13:44:53,142 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/ctdDriver.log (1921926 bytes) INFO 2025-06-26 13:44:53,280 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.325.16/ctdDriver.log: [ 22 826 1745 3596 4118 9844 15446 18098] INFO 2025-06-26 13:44:53,286 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/ctdDriver2.log (1921151 bytes) INFO 2025-06-26 13:44:53,427 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.325.16/ctdDriver2.log: [ 20 1352 2685 4110 6883 9835 10831 15436 17016 18090] INFO 2025-06-26 13:44:53,435 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/gps.log (23828 bytes) INFO 2025-06-26 13:44:53,445 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/hydroscatlog.log (1217414 bytes) INFO 2025-06-26 13:44:53,606 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.325.16/hydroscatlog.log: [ 3 5 6 43 49 63 64 80 81 87 106 110 113 162 303 411 453 456 508 548 572 613 756 780 785 806 904 945 1093 1134 1150 1388 1468 1469 1472 1476 1580 1660 1661 1868 2061 2169 2188 2304 2383 2502 2553 2832 3076 3216 3219 3387 3573 3717 3892 4276 4595 4754 4757 4758 4873 5228 5527 5927 6756 7073 7074 7377 7401 8222 8981 10037 10042 10270 10356 10370 10400 10476 10538 10542 10884 11023 11063 11146 11576 11664 12051 12297 12344 12774 13502 13714 15384 15385 15511 15512 15592 15690 15726 16424 17277 17382 18352 19477 19833 19942] INFO 2025-06-26 13:44:53,609 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/navigation.log (5891158 bytes) INFO 2025-06-26 13:44:54,052 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/isuslog.log (125269 bytes) INFO 2025-06-26 13:44:54,068 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/parosci.log (1971446 bytes) INFO 2025-06-26 13:44:54,230 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.325.16/parosci.log: [ 1 2 4 5 6 7 16 17 19 20 108 146 147 149 150 151 152 190 191 202 203 204 205 254 256 257 293 294 295 298 299 300 491 492 633 634 635 652 654 655 656 800 801 884 885 886 993 994 1120 1201 1202 1203 1204 1381 1382 1383 1487 1489 1490 1491 1492 1514 1515 1516 1544 1545 1546 1548 1549 1588 1589 1590 1788 1789 1790 1791 1829 2168 2170 2171 2172 2249 2250 2251 2253 2748 2927 2929 2930 2931 2953 3301 3302 3303 3305 3720 3721 3722 4112 4325 4327 4328 4329 4330 4347 4349 4350 4351 4352 4603 4604 4856 4857 4858 4999 5000 5001 5003 5100 5101 5102 5666 5667 5989 5990 6211 6438 6439 6440 6441 6778 6779 6780 6782 6783 7453 7455 7519 7520 7521 7808 8585 8586 8587 9232 9233 9234 9236 9237 9561 9563 9799 10512 10513 10514 10863 10864 13614 13616 13840 13841 13842 13844 13845 14239 14240 14241 14259 14260 14261 14873 14874 14876 14877 15786 15788 16594 16595 16596 18136 18668 18669 18670 18671 20286 20288 20667 20671 20752 20753 20754 20923 20925 20926 20927 20928 20951 20952 20953 21154 21155 21159 21160 21161 21162 21190 21191 21192 21193 21282 21283 21289 21290 21338 21392 21393 22258 22259 23291 23293 23370 23371 23372 23552 23553 24340 24840 24841 24842 24843 24933 24934 24935 25813 25814 27717 31120 31121 31123 31124 31125 31541 31542 31543 31544 31832 33225 33226 33227 33229 33566 33567 33569 33570 34960 34961 34962 34964 35175 35176 37152 37153 37154 37155 39450 39451 39452 39453 40164 40165 40166 40168 40169 40389 40390] INFO 2025-06-26 13:44:54,237 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/tailCone.log (242587 bytes) INFO 2025-06-26 13:44:54,274 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.325.16/biolume.log (1384620 bytes) INFO 2025-06-26 13:44:54,409 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:44:54,486 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.34 seconds WARNING 2025-06-26 13:44:54,486 process.py download_process():196 [1] No lopc.bin file for 2007.325.16 INFO 2025-06-26 13:44:54,486 process.py calibrate():227 [1] Calibration steps for 2007.325.16 INFO 2025-06-26 13:44:54,575 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 13:44:54,577 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:44:55,144 calibrate.py _nudge_pos():1806 [1] 88: 0.010 0.0003094 0.0000713 12115 40.93 1.121 0.323 2007-11-21T21:52:47.965452032 INFO 2025-06-26 13:44:56,154 calibrate.py _nudge_pos():1806 [1] 195: 0.030 0.0054123 -0.0003010 11283 37.80 21.249 -1.476 2007-11-21T22:32:23.962685184 INFO 2025-06-26 13:44:56,248 calibrate.py _nudge_pos():1806 [1] 205: 0.030 0.0000117 0.0000108 90 0.30 5.840 6.732 2007-11-21T22:32:50.960835584 INFO 2025-06-26 13:44:56,286 calibrate.py _nudge_pos():1806 [1] 209: 0.030 -0.0000288 -0.0000251 103 0.35 -12.328 -13.394 2007-11-21T22:33:14.959191552 INFO 2025-06-26 13:44:57,326 calibrate.py _nudge_pos():1862 [1] 284: - - - 0 0.00 - - INFO 2025-06-26 13:44:57,327 calibrate.py _nudge_pos():1868 [1] Points in final series = 24952 WARNING 2025-06-26 13:44:58,022 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 13:45:00,883 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:45:02,475 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 12 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:45:02,653 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 12 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:45:02,655 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.325.16/ctd1.nc INFO 2025-06-26 13:45:02,656 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 13:45:02,657 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 13:45:02,657 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:45:03,904 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 12 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:45:04,070 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 12 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 13:45:04,072 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.325.16/ctd2.nc INFO 2025-06-26 13:45:04,073 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd2_salinity values to NaN INFO 2025-06-26 13:45:04,074 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 13:45:04,074 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:45:04,089 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:45:04,467 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 298228 298229 298230] INFO 2025-06-26 13:45:04,518 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -9 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:45:04,525 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 13:45:04,526 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.325.16 ERROR 2025-06-26 13:45:04,526 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.325.16 INFO 2025-06-26 13:45:04,535 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_cal.nc INFO 2025-06-26 13:45:07,046 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_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, 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 13:45:07,052 process.py align():251 [1] Alignment steps for 2007.325.16 INFO 2025-06-26 13:45:07,081 align.py process_cal():139 [1] Processing dorado_2007.325.16_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.325.16 INFO 2025-06-26 13:45:07,099 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:45:07,102 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 13:45:07,136 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:45:07,139 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 13:45:07,173 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:45:07,176 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 13:45:07,194 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:45:07,194 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:45:07,206 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:45:07,209 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 13:45:07,241 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,244 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 13:45:07,271 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,274 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 13:45:07,299 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,303 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 13:45:07,328 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,333 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,362 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,367 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,397 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,401 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,431 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,434 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,462 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,465 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,494 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,497 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,525 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,528 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,559 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,563 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,590 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,593 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,641 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,644 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,671 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,674 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 13:45:07,704 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,707 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,739 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,743 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,770 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,773 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,801 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,805 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,834 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,838 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,866 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,871 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,899 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,903 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,931 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.325.16_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:45:07,935 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.95 INFO 2025-06-26 13:45:07,973 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:45:07,999 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:45:08,026 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 13:45:08,054 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:45:08,084 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 13:45:08,102 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_align.nc INFO 2025-06-26 13:45:08,176 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_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, 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 13:45:08,180 process.py resample():273 [1] Resampling steps for 2007.325.16 INFO 2025-06-26 13:45:08,181 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:45:08,216 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_align.nc mission netCDF file INFO 2025-06-26 13:45:08,222 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_align.nc mission netCDF file INFO 2025-06-26 13:45:08,224 resample.py get_mission_start_end():1145 [1] navigation: 2007-11-21T21:10:59.677281280 to 2007-11-21T22:35:03.961724160 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 13:45:08,227 resample.py get_mission_start_end():1145 [1] hs2 : 2007-11-21T21:10:32.999109120 to 2007-11-21T22:35:03.881729792 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 13:45:08,229 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-11-21T21:10:46.918155520 to 2007-11-21T22:35:04.051718144 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 13:45:08,232 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-11-21T21:10:46.958152704 to 2007-11-21T22:35:04.091715328 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:45:08,234 resample.py get_mission_start_end():1145 [1] isus : 2007-11-21T21:11:41.844392704 to 2007-11-21T22:35:03.591749632 (0 days 00:00:00.499965696 before mission_end) INFO 2025-06-26 13:45:08,236 resample.py get_mission_start_end():1145 [1] biolume : 2007-11-21T21:10:24.939627008 to 2007-11-21T22:35:02.641780480 (0 days 00:00:01.449934848 before mission_end) INFO 2025-06-26 13:45:08,238 resample.py get_mission_start_end():1145 [1] tailcone : 2007-11-21T21:10:32.409149440 to 2007-11-21T22:35:03.511755264 (0 days 00:00:00.579960064 before mission_end) INFO 2025-06-26 13:45:08,239 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_align.nc mission netCDF file INFO 2025-06-26 13:45:08,239 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,335 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,354 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,373 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,393 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,413 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,431 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,449 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,466 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,480 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,495 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,511 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,527 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,542 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,557 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,574 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,590 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,607 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,626 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,645 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,663 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,682 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,702 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,721 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,742 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,755 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,770 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,783 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,796 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,810 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:45:08,950 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_1S.nc INFO 2025-06-26 13:45:10,412 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 13:45:13,612 create_products.py gulper_odv():522 [1] Wrote 2 Gulper data lines to /data/auv_data/dorado/missionodvs/2007.325.16/dorado_2007.325.16_1S_Gulper.txt INFO 2025-06-26 13:45:13,612 process.py archive():337 [1] Archiving steps for 2007.325.16 INFO 2025-06-26 13:45:13,612 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16, BASE_PATH = /data/auv_data INFO 2025-06-26 13:45:13,612 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:45:13,614 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.325.16_1S.nc INFO 2025-06-26 13:45:13,625 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:45:13,626 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.325.16_cal.nc INFO 2025-06-26 13:45:13,654 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:45:13,655 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.325.16_align.nc INFO 2025-06-26 13:45:13,680 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:45:13,693 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,705 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,713 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,724 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,746 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,753 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,765 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,776 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,795 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007325/2007.325.16 done. INFO 2025-06-26 13:45:13,796 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:45:13,798 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2007/odv/dorado_2007.325.16_1S_Gulper.txt INFO 2025-06-26 13:45:13,803 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2007.325.16/dorado_2007.325.16_1S_Gulper.txt /Volumes/AUVCTD/surveys/2007/odv done. INFO 2025-06-26 13:45:13,803 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.325.16/dorado_2007.325.16_processing.log /Volumes/AUVCTD/surveys/2007/netcdf