INFO 2025-06-26 12:26:57,900 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 12:26:57,900 process.py process_mission():434 [1] dorado_info[mission]["comment"] = LOCO mission - HAB incubator area (off Soquel) - Zephyr prop damage to nosecone Got 'Error in plot_sections (line 852)' when reprocessed on 30 May 2018 - ctdToUse = ctd1 INFO 2025-06-26 12:26:57,900 process.py process_mission():449 [1] Processing LOCO mission 2006.348.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:26:57,900 process.py download_process():165 [1] Download and processing steps for 2006.348.01 INFO 2025-06-26 12:26:57,900 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006348/2006.348.01 INFO 2025-06-26 12:26:57,900 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006348/2006.348.01 to /data/auv_data/dorado/missionlogs/2006.348.01 INFO 2025-06-26 12:27:00,358 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.348.01 INFO 2025-06-26 12:27:00,358 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/ctdDriver.log (4349267 bytes) INFO 2025-06-26 12:27:00,667 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.348.01/ctdDriver.log: [ 1219 1903 2227 2911 5209 6343 7756 9594 11259 11597 12157 33074] INFO 2025-06-26 12:27:00,681 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/ctdDriver2.log (4349525 bytes) INFO 2025-06-26 12:27:00,997 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.348.01/ctdDriver2.log: [ 2230 2913 5331 6347 8017 9598 11600 33077] INFO 2025-06-26 12:27:01,015 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/gps.log (28220 bytes) INFO 2025-06-26 12:27:01,027 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/hydroscatlog.log (2970314 bytes) INFO 2025-06-26 12:27:01,379 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.348.01/hydroscatlog.log: [ 91 94 101 303 463 516 702 707 730 763 835 983 1049 1301 1526 1772 1837 1993 2319 2416 2812 3280 3311 3559 4152 4268 4447 4673 5102 5301 5445 6195 6231 6436 6785 7847 9636 11351 12046 12247 14563 14849 15767 16984 17483 18145 21041 21081 22947 24888 28005 30589 33155 35735 37328 37364 38081 39204 49171] INFO 2025-06-26 12:27:01,387 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/navigation.log (14548818 bytes) INFO 2025-06-26 12:27:02,448 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/isuslog.log (296789 bytes) INFO 2025-06-26 12:27:02,485 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/parosci.log (6366806 bytes) INFO 2025-06-26 12:27:03,037 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.348.01/parosci.log: [ 17 18 19 20 29 30 31 37 38 39 71 72 79 80 81 146 148 280 309 310 311 313 314 315 664 1125 1126 1303 1304 1445 1446 2104 2105 2106 2297 2462 2685 2686 2862 2864 2986 2988 2989 3323 3324 3539 4261 4262 4358 4359 4965 4966 4967 5036 5153 5383 5385 5903 5905 6250 6251 6253 6257 6937 7440 7441 7443 7510 7511 8903 9246 9247 9248 10491 10492 11152 11183 11184 11463 11941 12118 12119 12120 12546 12548 13184 13185 13691 13692 14229 14230 14232 14545 14546 14547 14615 14616 15714 15715 15716 15717 16625 16626 17268 18200 18201 18202 19781 19783 19784 20387 20388 21014 21738 21740 25084 25085 26640 27954 27955 27956 29262 29263 29658 29659 30221 30222 30430 30431 30432 32435 32436 32437 35105 35106 35107 37605 37607 38568 39035 39036 39037 39801 39803 40991 42267 42269 42270 44475 44477 45526 46862 46864 48638 48639 49650 49651 49652 52545 56400 56401 56403 61703 61704 68115 68116 68746 75050 75051 78654 78655 78656 78658 79702 81974 81975 81976 82109 82110 82111 84604 84605 84606 92277 92278 92282 92283 95781 99597 101590 101591 101592 102052 102053 102054 105063 105064 108977 114829 115685 115686 122638 122639 128293 129069 129070] INFO 2025-06-26 12:27:03,058 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/tailCone.log (2958571 bytes) INFO 2025-06-26 12:27:03,456 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.348.01/biolume.log (3372940 bytes) INFO 2025-06-26 12:27:03,774 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:27:03,960 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.60 seconds WARNING 2025-06-26 12:27:03,961 process.py download_process():196 [1] No lopc.bin file for 2006.348.01 INFO 2025-06-26 12:27:03,961 process.py calibrate():227 [1] Calibration steps for 2006.348.01 INFO 2025-06-26 12:27:04,097 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 12:27:04,098 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:27:04,670 calibrate.py _nudge_pos():1806 [1] 88: 0.060 -0.0004619 0.0006916 3641 12.26 -5.577 10.450 2006-12-14T16:11:23.805510144 INFO 2025-06-26 12:27:05,074 calibrate.py _nudge_pos():1806 [1] 130: 0.060 -0.0001406 0.0010313 6781 22.71 -0.916 8.413 2006-12-14T16:34:47.809329152 INFO 2025-06-26 12:27:05,446 calibrate.py _nudge_pos():1806 [1] 169: 0.070 0.0001559 0.0004811 6009 20.06 1.150 4.444 2006-12-14T16:55:29.804246784 INFO 2025-06-26 12:27:05,872 calibrate.py _nudge_pos():1806 [1] 212: 0.080 -0.0000071 -0.0000209 6678 22.30 -0.047 -0.174 2006-12-14T17:18:29.799710464 INFO 2025-06-26 12:27:06,251 calibrate.py _nudge_pos():1806 [1] 251: 0.070 -0.0003698 -0.0003793 7837 26.18 -2.092 -2.684 2006-12-14T17:45:18.809485568 INFO 2025-06-26 12:27:06,558 calibrate.py _nudge_pos():1806 [1] 283: 0.080 -0.0002540 -0.0000638 10270 34.26 -1.098 -0.345 2006-12-14T18:20:05.806516736 INFO 2025-06-26 12:27:06,917 calibrate.py _nudge_pos():1806 [1] 321: 0.080 -0.0004075 -0.0001148 9558 31.88 -1.894 -0.667 2006-12-14T18:52:35.802932736 INFO 2025-06-26 12:27:07,286 calibrate.py _nudge_pos():1806 [1] 360: 0.090 -0.0001388 -0.0000046 9194 30.66 -0.671 -0.028 2006-12-14T19:23:53.804280832 INFO 2025-06-26 12:27:07,476 calibrate.py _nudge_pos():1862 [1] 345: - - - 0 0.00 - - INFO 2025-06-26 12:27:07,476 calibrate.py _nudge_pos():1868 [1] Points in final series = 61638 WARNING 2025-06-26 12:27:09,626 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:27:16,205 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:19,730 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:20,104 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:20,106 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.348.01/ctd1.nc INFO 2025-06-26 12:27:20,107 calibrate.py _range_qc_combined_nc():898 [1] Setting 258 ctd1_salinity values to NaN INFO 2025-06-26 12:27:20,107 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 12:27:20,107 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:27:22,865 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:23,247 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:27:23,249 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.348.01/ctd2.nc INFO 2025-06-26 12:27:23,251 calibrate.py _range_qc_combined_nc():898 [1] Setting 167 ctd2_salinity values to NaN INFO 2025-06-26 12:27:23,251 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 12:27:23,251 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:27:23,274 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:27:23,805 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 719104 719105 719106] INFO 2025-06-26 12:27:23,917 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:27:23,922 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 12:27:23,922 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.348.01 ERROR 2025-06-26 12:27:23,923 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.348.01 INFO 2025-06-26 12:27:23,973 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_cal.nc INFO 2025-06-26 12:27:27,843 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 12:27:27,847 process.py align():251 [1] Alignment steps for 2006.348.01 INFO 2025-06-26 12:27:27,939 align.py process_cal():139 [1] Processing dorado_2006.348.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.348.01 INFO 2025-06-26 12:27:27,958 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:27,961 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:28,007 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:28,011 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:28,057 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:28,062 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:28,089 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:27:28,089 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:27:28,107 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:27:28,110 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:27:28,153 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:27:28,157 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:28,196 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:27:28,200 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:28,240 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:27:28,244 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:27:28,284 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,287 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,327 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,330 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,370 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,373 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,412 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,415 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,455 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,459 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,500 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,504 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,544 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,547 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,588 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,592 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,632 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,636 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,675 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,678 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,717 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,721 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,766 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,771 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,816 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,820 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,864 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,868 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,908 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,911 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,952 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,955 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:28,995 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.348.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:27:28,998 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:27:29,051 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:27:29,088 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:27:29,125 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.75 INFO 2025-06-26 12:27:29,164 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:27:29,205 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:27:29,239 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_align.nc INFO 2025-06-26 12:27:29,304 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 12:27:29,306 process.py resample():273 [1] Resampling steps for 2006.348.01 INFO 2025-06-26 12:27:29,307 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:27:29,331 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_align.nc mission netCDF file INFO 2025-06-26 12:27:29,336 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_align.nc mission netCDF file INFO 2025-06-26 12:27:29,337 resample.py get_mission_start_end():1145 [1] navigation: 2006-12-14T15:58:16.259460352 to 2006-12-14T19:24:12.802979328 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 12:27:29,339 resample.py get_mission_start_end():1145 [1] hs2 : 2006-12-14T15:57:54.330962688 to 2006-12-14T19:24:12.812978688 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 12:27:29,340 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-12-14T15:58:14.859556352 to 2006-12-14T19:24:12.842976512 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:27:29,342 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-12-14T15:58:14.839557888 to 2006-12-14T19:24:12.812978688 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 12:27:29,344 resample.py get_mission_start_end():1145 [1] isus : 2006-12-14T15:58:59.266514176 to 2006-12-14T19:24:11.993034752 (0 days 00:00:00.849941760 before mission_end) INFO 2025-06-26 12:27:29,345 resample.py get_mission_start_end():1145 [1] biolume : 2006-12-14T15:57:45.381541376 to 2006-12-14T19:24:11.893007616 (0 days 00:00:00.949968896 before mission_end) INFO 2025-06-26 12:27:29,346 resample.py get_mission_start_end():1145 [1] tailcone : 2006-12-14T15:57:44.091664128 to 2006-12-14T19:24:12.812978688 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 12:27:29,347 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_align.nc mission netCDF file INFO 2025-06-26 12:27:29,348 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,504 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,531 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,557 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,583 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,609 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,634 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,658 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,681 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,702 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,726 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,747 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,769 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,790 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,811 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,833 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,854 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,878 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,900 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,923 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,944 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,966 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:29,988 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:30,001 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:30,014 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:30,027 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:30,040 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:30,067 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:27:30,234 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_1S.nc INFO 2025-06-26 12:27:31,825 create_products.py gulper_odv():401 [1] No gulper times found for 2006.348.01 INFO 2025-06-26 12:27:31,825 process.py archive():337 [1] Archiving steps for 2006.348.01 INFO 2025-06-26 12:27:31,825 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01, BASE_PATH = /data/auv_data INFO 2025-06-26 12:27:31,825 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 12:27:31,827 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.348.01_1S.nc INFO 2025-06-26 12:27:31,843 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:27:31,844 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.348.01_cal.nc INFO 2025-06-26 12:27:31,903 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:27:31,903 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.348.01_align.nc INFO 2025-06-26 12:27:31,954 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 12:27:31,971 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:31,988 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:31,992 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,005 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,045 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,051 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,074 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,089 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,124 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006348/2006.348.01 done. INFO 2025-06-26 12:27:32,125 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:27:32,125 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.348.01/dorado_2006.348.01_processing.log /Volumes/AUVCTD/surveys/2006/netcdf