INFO 2025-06-26 12:31:22,571 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 12:31:22,571 process.py process_mission():434 [1] dorado_info[mission]["comment"] = BIOLUME mission - First real mission with new blunt nose cone - Zephr attended to dorado at M1 in the morning - ctdToUse = ctd1 INFO 2025-06-26 12:31:22,571 process.py process_mission():449 [1] Processing BIOLUME mission 2007.067.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:31:22,571 process.py download_process():165 [1] Download and processing steps for 2007.067.01 INFO 2025-06-26 12:31:22,571 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007067/2007.067.01 INFO 2025-06-26 12:31:22,571 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007067/2007.067.01 to /data/auv_data/dorado/missionlogs/2007.067.01 INFO 2025-06-26 12:31:25,599 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.067.01 INFO 2025-06-26 12:31:25,599 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/ctdDriver.log (7834331 bytes) INFO 2025-06-26 12:31:26,262 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.067.01/ctdDriver.log: [ 4 1018 1099 3669 4100 4825 5188 5902 6564 7544 11475 13031 15393 23889 31427 35739 36202 42792 59443 59585 68137 75277 78220] INFO 2025-06-26 12:31:26,313 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/ctdDriver2.log (7833973 bytes) INFO 2025-06-26 12:31:26,973 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.067.01/ctdDriver2.log: [ 3 1018 1099 1878 4102 6565 7545 11287 11477 13033 15395 22139 23893 36207 42794 44348 75272 78215] INFO 2025-06-26 12:31:27,029 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/gps.log (46148 bytes) INFO 2025-06-26 12:31:27,044 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/hydroscatlog.log (5350514 bytes) INFO 2025-06-26 12:31:27,758 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.067.01/hydroscatlog.log: [ 1096 2014 2081 2465 2693 3084 3086 3102 3382 3758 4279 4908 6423 6746 6834 7399 7621 7643 8227 8299 8997 9639 10196 11585 11931 12665 14443 14444 14834 16679 20990 21418 22258 23536 24015 29707 29979 30417 33386 36334 38183 45574 46108 49548 50124 51981 59433 59476 59578 60070 65167 67970 68051 74314 75735 76659 80434 88109] INFO 2025-06-26 12:31:27,784 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/navigation.log (26254418 bytes) INFO 2025-06-26 12:31:30,035 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/isuslog.log (504341 bytes) INFO 2025-06-26 12:31:30,094 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/parosci.log (11485286 bytes) INFO 2025-06-26 12:31:31,109 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.067.01/parosci.log: [ 16 17 18 19 40 59 60 61 63 64 89 105 106 346 997 2043 2044 2289 3274 3275 3408 3801 3802 3803 4684 5297 5298 5541 5542 5721 5723 5727 5729 6755 6879 6880 6882 7895 8133 8134 8135 8421 8422 8464 8465 8467 9220 9784 11240 11387 11388 12200 12202 12203 12448 12893 12894 12895 13072 13073 13074 13311 13334 14565 14567 17382 17383 17384 18253 18255 18256 18472 18473 19600 21774 22225 22226 22419 22420 26013 26945 26946 26947 27505 27507 28079 28751 28752 29949 30309 30310 30311 30312 31242 31243 32480 34149 37315 37316 38925 38926 39970 39972 41780 44236 44581 48144 54694 57670 59123 62623 63171 63352 64843 68612 69952 69953 69955 69956 72208 72210 72211 76279 79264 79909 79910 79911 80143 80144 81811 81812 81813 96090 96092 96444 96445 96446 98661 98663 101528 102647 102648 102649 115351 115352 115899 115901 115902 119806 120577 122441 123878 133099 134519 134646 134647 139622 139623 158692 158693 158695 159702 161291 161292 172344 172345 174949 174950 179811 182465 182466 196812 196813 199635 199914 199915 200458 200459 200461 200462 203280 203281 205755 210314 224229 224230 224231 224232 228189 228191 230403 234943 236449 236450 236451 236453] INFO 2025-06-26 12:31:31,164 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/tailCone.log (5338843 bytes) INFO 2025-06-26 12:31:31,921 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.067.01/biolume.log (6072812 bytes) INFO 2025-06-26 12:31:32,538 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:31:32,905 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.31 seconds WARNING 2025-06-26 12:31:32,905 process.py download_process():196 [1] No lopc.bin file for 2007.067.01 INFO 2025-06-26 12:31:32,906 process.py calibrate():227 [1] Calibration steps for 2007.067.01 INFO 2025-06-26 12:31:33,136 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 12:31:33,139 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:31:33,949 calibrate.py _nudge_pos():1806 [1] 108: 0.160 -0.0038594 0.0021690 11258 37.68 -15.201 10.667 2007-03-08T17:18:11.812384768 INFO 2025-06-26 12:31:34,409 calibrate.py _nudge_pos():1806 [1] 153: 0.150 -0.0017349 0.0009816 5765 19.26 -13.364 9.442 2007-03-08T17:38:11.820178688 INFO 2025-06-26 12:31:34,920 calibrate.py _nudge_pos():1806 [1] 199: 0.160 -0.0039683 0.0017287 12506 41.75 -14.100 7.673 2007-03-08T18:20:41.815492096 INFO 2025-06-26 12:31:35,424 calibrate.py _nudge_pos():1806 [1] 246: 0.170 -0.0032754 0.0014771 12025 40.13 -12.102 6.820 2007-03-08T19:01:35.817381376 INFO 2025-06-26 12:31:35,924 calibrate.py _nudge_pos():1806 [1] 287: 0.170 -0.0030174 0.0014435 11097 37.03 -12.078 7.223 2007-03-08T19:39:17.812424192 INFO 2025-06-26 12:31:36,418 calibrate.py _nudge_pos():1806 [1] 332: 0.180 -0.0035087 0.0015403 12068 40.26 -12.912 7.089 2007-03-08T20:20:17.813902336 INFO 2025-06-26 12:31:36,864 calibrate.py _nudge_pos():1806 [1] 373: 0.180 -0.0023088 0.0011063 8586 28.63 -11.946 7.160 2007-03-08T20:49:35.813471232 INFO 2025-06-26 12:31:37,334 calibrate.py _nudge_pos():1806 [1] 414: 0.170 -0.0004783 0.0004182 2859 9.53 -7.434 8.132 2007-03-08T20:59:47.821545728 INFO 2025-06-26 12:31:37,816 calibrate.py _nudge_pos():1806 [1] 458: 0.180 -0.0000365 0.0015829 5716 19.08 -0.283 15.373 2007-03-08T21:19:35.820162304 INFO 2025-06-26 12:31:38,351 calibrate.py _nudge_pos():1806 [1] 509: 0.190 -0.0003400 0.0019723 6138 20.46 -2.461 17.860 2007-03-08T21:40:53.812613888 INFO 2025-06-26 12:31:38,811 calibrate.py _nudge_pos():1806 [1] 552: 0.180 -0.0006583 -0.0006299 10969 36.60 -2.665 -3.190 2007-03-08T22:18:11.819299840 INFO 2025-06-26 12:31:39,401 calibrate.py _nudge_pos():1806 [1] 610: 0.190 -0.0010686 -0.0008406 9368 31.25 -5.069 -4.985 2007-03-08T22:50:23.816949248 INFO 2025-06-26 12:31:39,603 calibrate.py _nudge_pos():1862 [1] 591: - - - 1 0.00 - - INFO 2025-06-26 12:31:39,603 calibrate.py _nudge_pos():1868 [1] Points in final series = 111239 WARNING 2025-06-26 12:31:43,788 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 12:31:55,399 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 89102 INFO 2025-06-26 12:31:56,090 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 14 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:32:02,623 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 32 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:32:03,291 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 32 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:32:03,294 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.067.01/ctd1.nc INFO 2025-06-26 12:32:03,295 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:32:03,295 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 12:32:03,296 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:32:08,279 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 32 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:32:08,960 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 32 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:32:08,963 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.067.01/ctd2.nc WARNING 2025-06-26 12:32:08,965 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (19383) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 12:32:08,965 calibrate.py _range_qc_combined_nc():898 [1] Setting 19383 ctd2_salinity values to NaN INFO 2025-06-26 12:32:08,966 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 12:32:08,966 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:32:09,003 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:32:10,049 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 1289346 1289347 1289348] INFO 2025-06-26 12:32:10,253 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:32:10,259 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 12:32:10,259 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.067.01 ERROR 2025-06-26 12:32:10,259 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.067.01 INFO 2025-06-26 12:32:10,349 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_cal.nc INFO 2025-06-26 12:32:17,433 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 12:32:17,438 process.py align():251 [1] Alignment steps for 2007.067.01 INFO 2025-06-26 12:32:17,467 align.py process_cal():139 [1] Processing dorado_2007.067.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.067.01 INFO 2025-06-26 12:32:17,498 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:32:17,503 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:32:17,579 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:32:17,584 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:32:17,657 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:32:17,662 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:32:17,709 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:32:17,709 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:32:17,737 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:32:17,742 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 12:32:17,812 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:32:17,817 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:32:17,881 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:32:17,886 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:32:17,949 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 12:32:17,954 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 12:32:18,019 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,024 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,088 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,093 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,156 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,161 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,228 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,233 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,296 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,301 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,364 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,369 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,433 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,438 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,504 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,509 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,574 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,579 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,644 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,648 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,712 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,716 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,781 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,785 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,849 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,854 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,918 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,923 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:18,986 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:18,990 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:19,055 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:19,060 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:19,124 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.067.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 12:32:19,128 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 12:32:19,209 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:32:19,264 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:32:19,320 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:32:19,377 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:32:19,439 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 12:32:19,492 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_align.nc INFO 2025-06-26 12:32:19,586 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 12:32:19,589 process.py resample():273 [1] Resampling steps for 2007.067.01 INFO 2025-06-26 12:32:19,589 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:32:19,617 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_align.nc mission netCDF file INFO 2025-06-26 12:32:19,623 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_align.nc mission netCDF file INFO 2025-06-26 12:32:19,625 resample.py get_mission_start_end():1145 [1] navigation: 2007-03-08T16:39:22.511952896 to 2007-03-08T22:50:42.015702272 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:32:19,627 resample.py get_mission_start_end():1145 [1] hs2 : 2007-03-08T16:39:01.373400832 to 2007-03-08T22:50:41.815716096 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 12:32:19,628 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-03-08T16:39:18.982194688 to 2007-03-08T22:50:42.015702272 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:32:19,630 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-03-08T16:39:19.222178304 to 2007-03-08T22:50:41.955706368 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 12:32:19,632 resample.py get_mission_start_end():1145 [1] isus : 2007-03-08T16:40:04.109103104 to 2007-03-08T22:50:41.315750400 (0 days 00:00:00.699951872 before mission_end) INFO 2025-06-26 12:32:19,633 resample.py get_mission_start_end():1145 [1] biolume : 2007-03-08T16:38:49.114206464 to 2007-03-08T22:50:40.995738112 (0 days 00:00:01.019964160 before mission_end) INFO 2025-06-26 12:32:19,635 resample.py get_mission_start_end():1145 [1] tailcone : 2007-03-08T16:38:47.714336512 to 2007-03-08T22:50:41.815716096 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 12:32:19,636 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_align.nc mission netCDF file INFO 2025-06-26 12:32:19,636 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:19,881 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:19,924 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:19,966 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,010 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,048 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,085 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,121 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,156 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,190 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,223 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,255 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,289 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,322 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,354 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,386 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,418 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,454 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,488 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,562 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,597 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,632 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,667 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,684 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,699 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,713 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,729 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,769 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:32:20,992 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_1S.nc INFO 2025-06-26 12:32:22,041 create_products.py gulper_odv():401 [1] No gulper times found for 2007.067.01 INFO 2025-06-26 12:32:22,041 process.py archive():337 [1] Archiving steps for 2007.067.01 INFO 2025-06-26 12:32:22,041 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01, BASE_PATH = /data/auv_data INFO 2025-06-26 12:32:22,043 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:32:22,044 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.067.01_1S.nc INFO 2025-06-26 12:32:22,067 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:32:22,068 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.067.01_cal.nc INFO 2025-06-26 12:32:22,171 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:32:22,172 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.067.01_align.nc INFO 2025-06-26 12:32:22,269 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:32:22,297 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,322 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,326 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,346 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,421 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,428 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,466 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,489 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,555 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007067/2007.067.01 done. INFO 2025-06-26 12:32:22,555 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:32:22,556 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.067.01/dorado_2007.067.01_processing.log /Volumes/AUVCTD/surveys/2007/netcdf