INFO 2025-06-26 12:26:03,836 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 12:26:03,836 process.py process_mission():434 [1] dorado_info[mission]["comment"] = LOCO mission - HAB incubator area (off Soquel) - ctdToUse = ctd1 INFO 2025-06-26 12:26:03,836 process.py process_mission():449 [1] Processing LOCO mission 2006.347.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:26:03,836 process.py download_process():165 [1] Download and processing steps for 2006.347.05 INFO 2025-06-26 12:26:03,836 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006347/2006.347.05 INFO 2025-06-26 12:26:03,836 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006347/2006.347.05 to /data/auv_data/dorado/missionlogs/2006.347.05 INFO 2025-06-26 12:26:06,612 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.347.05 INFO 2025-06-26 12:26:06,612 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/ctdDriver.log (7076915 bytes) INFO 2025-06-26 12:26:07,143 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.347.05/ctdDriver.log: [ 8 751 817 1781 1902 2527 5012 5245 8017 10374 13275 13335 16203 23068 32863 42522 50028 77932] INFO 2025-06-26 12:26:07,166 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/ctdDriver2.log (7076821 bytes) INFO 2025-06-26 12:26:07,680 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.347.05/ctdDriver2.log: [ 624 748 815 1483 2226 3506 5602 6353 6702 8013 23111 25136 34750 40067 42523 42524 42963 62466 63903 77933] INFO 2025-06-26 12:26:07,708 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/gps.log (46796 bytes) INFO 2025-06-26 12:26:07,722 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/hydroscatlog.log (4829414 bytes) INFO 2025-06-26 12:26:08,286 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.347.05/hydroscatlog.log: [ 3 10 42 237 300 325 527 550 646 740 774 845 988 1588 1617 1800 1997 2250 2323 2410 2494 3509 3604 4523 5456 6255 7314 8017 8123 8304 8507 10906 11177 11181 12064 13264 13370 13430 13876 15450 15564 16297 19135 27597 28437 31730 32337 34728 34834 36023 36441 39454 43045 43156 46562 48031 50108 53671 55315 56190 56576 57021 58683 63298 63976 73190 76718 77998] INFO 2025-06-26 12:26:08,299 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/navigation.log (23684142 bytes) INFO 2025-06-26 12:26:10,019 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/isuslog.log (483797 bytes) INFO 2025-06-26 12:26:10,070 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.347.05/isuslog.log: [1 2 3 5 6 7 8 9] INFO 2025-06-26 12:26:10,072 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/parosci.log (10353974 bytes) INFO 2025-06-26 12:26:10,951 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.347.05/parosci.log: [ 3 4 16 18 19 20 64 148 149 303 366 368 843 844 886 1444 1446 1447 1509 1766 1767 2018 2110 2296 2678 2679 2935 3131 3133 3549 3550 3551 4138 4277 4689 4690 4691 4779 4781 4843 4844 5047 5372 6004 6046 6047 6267 6378 6471 6697 6884 7035 7036 7037 7231 8072 8900 8901 8902 8968 8969 8970 9040 9209 9211 9232 9234 10533 10534 10785 10786 12358 14306 14308 14506 14507 14622 15272 15803 15804 15805 16106 16107 16108 19598 19599 20022 20023 20024 20025 20406 20408 20409 22798 22799 23696 23697 23698 24062 27525 27526 27527 28045 28047 29961 32613 35536 35537 35538 35820 37175 41696 41697 43642 43643 43644 43665 44826 44828 47989 48514 48515 50889 50891 51264 51265 53285 53286 53821 56189 56190 59109 61651 62053 62054 62134 62135 62169 64401 64402 64403 65510 65511 67590 68158 68159 68160 73947 73948 73950 76204 76206 76887 79657 86656 88293 88294 93348 93349 96532 96533 96534 100527 100993 100995 100996 105723 105724 105725 107595 114075 114076 114177 115650 115651 115652 122370 122371 129845 134289 134291 140115 140116 143845 145510 145511 145512 148250 148252 150599 151632 151633 157275 162917 162918 162919 165932 167608 169645 171462 171463 171464 172411 172412 174505 194593 194594 196168 196169 205627 205628 209057] INFO 2025-06-26 12:26:10,985 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/tailCone.log (4815499 bytes) INFO 2025-06-26 12:26:11,608 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.347.05/biolume.log (5480124 bytes) INFO 2025-06-26 12:26:12,145 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:26:12,438 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.83 seconds WARNING 2025-06-26 12:26:12,438 process.py download_process():196 [1] No lopc.bin file for 2006.347.05 INFO 2025-06-26 12:26:12,438 process.py calibrate():227 [1] Calibration steps for 2006.347.05 INFO 2025-06-26 12:26:12,615 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 12:26:12,617 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:26:13,234 calibrate.py _nudge_pos():1806 [1] 89: 0.180 -0.0007814 0.0004335 2788 9.39 -12.322 8.555 2006-12-13T17:59:53.468372736 INFO 2025-06-26 12:26:13,747 calibrate.py _nudge_pos():1806 [1] 143: 0.180 -0.0001028 0.0010510 7203 24.11 -0.631 8.076 2006-12-13T18:24:53.465615872 INFO 2025-06-26 12:26:13,757 calibrate.py _nudge_pos():1806 [1] 144: 0.190 0.0000088 0.0000121 70 0.23 5.673 9.739 2006-12-13T18:25:07.464657152 INFO 2025-06-26 12:26:14,166 calibrate.py _nudge_pos():1806 [1] 187: 0.190 0.0001690 0.0004300 5938 19.85 1.261 4.015 2006-12-13T18:45:41.470121984 INFO 2025-06-26 12:26:14,629 calibrate.py _nudge_pos():1806 [1] 235: 0.190 -0.0000151 0.0000168 6833 22.81 -0.098 0.137 2006-12-13T19:09:17.463119872 INFO 2025-06-26 12:26:14,707 calibrate.py _nudge_pos():1806 [1] 243: 0.190 -0.0000606 0.0000024 30 0.10 -92.834 4.547 2006-12-13T19:09:30.462229248 INFO 2025-06-26 12:26:15,041 calibrate.py _nudge_pos():1806 [1] 278: 0.200 -0.0002287 -0.0001675 7793 26.01 -1.302 -1.193 2006-12-13T19:36:05.462964224 INFO 2025-06-26 12:26:15,051 calibrate.py _nudge_pos():1806 [1] 279: 0.200 0.0000003 0.0000031 54 0.18 0.231 3.207 2006-12-13T19:36:16.462210560 INFO 2025-06-26 12:26:15,515 calibrate.py _nudge_pos():1806 [1] 327: 0.200 -0.0009968 -0.0005557 10800 36.03 -4.099 -2.858 2006-12-13T20:13:05.460883968 INFO 2025-06-26 12:26:15,525 calibrate.py _nudge_pos():1806 [1] 328: 0.190 -0.0000127 -0.0000913 29 0.09 -20.180 -181.045 2006-12-13T20:13:11.470472448 INFO 2025-06-26 12:26:15,974 calibrate.py _nudge_pos():1806 [1] 374: 0.200 -0.0010252 -0.0005040 10027 33.45 -4.542 -2.792 2006-12-13T20:47:23.469900544 INFO 2025-06-26 12:26:15,995 calibrate.py _nudge_pos():1806 [1] 376: 0.200 0.0000237 -0.0000276 69 0.23 15.473 -22.597 2006-12-13T20:47:38.468873216 INFO 2025-06-26 12:26:16,420 calibrate.py _nudge_pos():1806 [1] 418: 0.010 -0.0008059 -0.0001843 10152 33.86 -3.527 -1.008 2006-12-13T21:22:11.666849280 INFO 2025-06-26 12:26:16,479 calibrate.py _nudge_pos():1806 [1] 424: 0.010 -0.0000439 0.0000093 50 0.16 -39.874 10.593 2006-12-13T21:22:26.665821696 INFO 2025-06-26 12:26:16,830 calibrate.py _nudge_pos():1806 [1] 460: 0.010 -0.0011761 -0.0004688 11168 37.26 -4.679 -2.331 2006-12-13T22:00:17.670247424 INFO 2025-06-26 12:26:17,391 calibrate.py _nudge_pos():1806 [1] 518: 0.020 -0.0010969 -0.0003779 9336 31.15 -5.222 -2.249 2006-12-13T22:32:23.668307456 INFO 2025-06-26 12:26:17,422 calibrate.py _nudge_pos():1806 [1] 521: 0.010 -0.0000319 -0.0000054 55 0.18 -26.300 -5.544 2006-12-13T22:32:36.667417088 INFO 2025-06-26 12:26:17,801 calibrate.py _nudge_pos():1806 [1] 560: 0.020 -0.0011730 -0.0004253 10721 35.75 -4.867 -2.204 2006-12-13T23:08:59.667871232 INFO 2025-06-26 12:26:18,212 calibrate.py _nudge_pos():1806 [1] 601: 0.020 -0.0003960 -0.0001832 4300 14.33 -4.099 -2.369 2006-12-13T23:23:59.666217216 INFO 2025-06-26 12:26:18,576 calibrate.py _nudge_pos():1862 [1] 605: - - - 2 0.00 - - INFO 2025-06-26 12:26:18,576 calibrate.py _nudge_pos():1868 [1] Points in final series = 100236 WARNING 2025-06-26 12:26:22,060 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:26:32,209 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 308 of 80407 INFO 2025-06-26 12:26:32,829 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:26:38,616 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:26:39,216 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:26:39,219 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.347.05/ctd1.nc INFO 2025-06-26 12:26:39,220 calibrate.py _range_qc_combined_nc():898 [1] Setting 316 ctd1_salinity values to NaN INFO 2025-06-26 12:26:39,220 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 12:26:39,220 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:26:43,633 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:26:44,245 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:26:44,247 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.347.05/ctd2.nc INFO 2025-06-26 12:26:44,248 calibrate.py _range_qc_combined_nc():898 [1] Setting 152 ctd2_salinity values to NaN INFO 2025-06-26 12:26:44,248 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 12:26:44,249 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:26:44,971 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:26:45,910 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 1126152 1202580 1202581] INFO 2025-06-26 12:26:46,090 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:26:46,095 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 12:26:46,096 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.347.05 ERROR 2025-06-26 12:26:46,096 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.347.05 INFO 2025-06-26 12:26:46,176 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_cal.nc INFO 2025-06-26 12:26:52,425 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 12:26:52,429 process.py align():251 [1] Alignment steps for 2006.347.05 INFO 2025-06-26 12:26:52,459 align.py process_cal():139 [1] Processing dorado_2006.347.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.347.05 INFO 2025-06-26 12:26:52,488 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:26:52,492 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:26:52,560 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:26:52,565 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:26:52,632 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:26:52,637 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:26:52,677 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:26:52,677 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:26:52,704 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:26:52,709 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:26:52,773 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:26:52,777 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:26:52,835 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:26:52,840 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:26:52,900 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:26:52,904 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:26:52,962 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:52,966 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,026 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,030 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,089 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,094 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,152 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,157 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,215 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,219 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,291 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,296 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,355 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,360 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,418 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,423 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,480 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,484 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,543 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,547 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,607 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,612 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,671 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,676 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,734 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,739 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,798 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,803 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,861 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,865 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,924 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,929 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:53,987 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.347.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:26:53,991 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:26:54,065 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:26:54,116 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:26:54,167 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:26:54,221 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:26:54,279 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:26:54,326 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_align.nc INFO 2025-06-26 12:26:54,405 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 12:26:54,408 process.py resample():273 [1] Resampling steps for 2006.347.05 INFO 2025-06-26 12:26:54,408 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:26:54,498 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_align.nc mission netCDF file INFO 2025-06-26 12:26:54,504 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_align.nc mission netCDF file INFO 2025-06-26 12:26:54,505 resample.py get_mission_start_end():1145 [1] navigation: 2006-12-13T17:49:34.960743680 to 2006-12-13T23:24:36.063723776 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 12:26:54,507 resample.py get_mission_start_end():1145 [1] hs2 : 2006-12-13T17:49:08.032588288 to 2006-12-13T23:24:36.093721600 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 12:26:54,509 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-12-13T17:49:31.540977920 to 2006-12-13T23:24:36.133719040 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:26:54,510 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-12-13T17:49:32.420917504 to 2006-12-13T23:24:35.983729152 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 12:26:54,512 resample.py get_mission_start_end():1145 [1] isus : 2006-12-13T17:50:03.608781056 to 2006-12-13T23:24:35.353772288 (0 days 00:00:00.779946752 before mission_end) INFO 2025-06-26 12:26:54,513 resample.py get_mission_start_end():1145 [1] biolume : 2006-12-13T17:49:02.032964864 to 2006-12-13T23:24:35.443731968 (0 days 00:00:00.689987072 before mission_end) INFO 2025-06-26 12:26:54,515 resample.py get_mission_start_end():1145 [1] tailcone : 2006-12-13T17:49:05.062791936 to 2006-12-13T23:24:36.033725696 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 12:26:54,515 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_align.nc mission netCDF file INFO 2025-06-26 12:26:54,516 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,753 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,792 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,831 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,869 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,903 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,935 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:54,968 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,000 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,032 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,064 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,094 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,124 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,155 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,184 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,214 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,243 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,276 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,307 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,340 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,371 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,403 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,435 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,450 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,465 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,479 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,494 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,532 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:26:55,741 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_1S.nc INFO 2025-06-26 12:26:57,386 create_products.py gulper_odv():401 [1] No gulper times found for 2006.347.05 INFO 2025-06-26 12:26:57,386 process.py archive():337 [1] Archiving steps for 2006.347.05 INFO 2025-06-26 12:26:57,386 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05, BASE_PATH = /data/auv_data INFO 2025-06-26 12:26:57,388 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 12:26:57,389 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.347.05_1S.nc INFO 2025-06-26 12:26:57,411 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:26:57,413 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.347.05_cal.nc INFO 2025-06-26 12:26:57,509 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:26:57,510 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.347.05_align.nc INFO 2025-06-26 12:26:57,598 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:26:57,624 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,649 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,654 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,672 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,748 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,755 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,787 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,807 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,865 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006347/2006.347.05 done. INFO 2025-06-26 12:26:57,865 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:26:57,865 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.347.05/dorado_2006.347.05_processing.log /Volumes/AUVCTD/surveys/2006/netcdf