INFO 2025-06-26 13:04:21,352 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 13:04:21,352 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Internal wave study near Monterey - ctdToUse = ctd1 INFO 2025-06-26 13:04:21,352 process.py process_mission():449 [1] Processing AUVCTD mission 2007.239.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 13:04:21,352 process.py download_process():165 [1] Download and processing steps for 2007.239.05 INFO 2025-06-26 13:04:21,352 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007239/2007.239.05 INFO 2025-06-26 13:04:21,352 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007239/2007.239.05 to /data/auv_data/dorado/missionlogs/2007.239.05 INFO 2025-06-26 13:04:27,069 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.239.05 INFO 2025-06-26 13:04:27,069 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/ctdDriver.log (22300827 bytes) INFO 2025-06-26 13:04:28,680 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.239.05/ctdDriver.log: [ 235 389 438 460 520 702 805 840 971 1284 1530 1687 1973 1980 2073 2084 2230 2287 2569 3008 3232 3420 3801 4790 4892 4973 4990 5018 5367 5850 6854 7383 7658 8783 9327 10298 10427 11134 11270 11355 11411 13182 14857 15713 16221 17168 17550 17608 17609 18248 22224 22442 23208 23899 24290 25351 26414 26472 27283 27655 28015 31954 33299 33626 34793 35869 39481 39702 43098 45644 49813 52756 54119 57967 59279 60216 61225 61836 63250 63522 64815 69968 74107 76682 77908 79812 81219 83396 85672 87310 88332 90362 93425 94232 97834 102557 103421 103540 110254 113365 116154 116780 117765 123683 123896 130129 130399 132171 132315 133297 133337 135591 137114 138126 143239 145244 152662 153215 157631 164321 170696 173697 177049 177326 177412 177564 190844 192328 193094 195045 197565 199107 199835 202161 203057 204282 207337 209275 210997 213058 214943 216389 217435 223006 223343 224430 224653 228664 230616 231146 233034 237340 244840 244844 247629 249241 249242 252344] INFO 2025-06-26 13:04:28,755 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/ctdDriver2.log (22299149 bytes) INFO 2025-06-26 13:04:30,410 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.239.05/ctdDriver2.log: [ 149 238 391 441 463 522 687 702 806 840 970 1023 1281 1491 1528 1687 1974 1980 2083 2287 2569 3008 3155 3231 3417 3798 3882 4886 4967 4983 5359 5842 5973 6847 7376 7650 8961 10291 10419 11127 11332 11346 11402 13174 14850 15706 16206 16213 17158 17596 18236 22427 23192 26456 27215 27268 27641 28001 30236 31940 33284 33611 38020 39466 41720 43083 43567 45353 45630 49800 52744 54109 57957 60206 61215 63175 63239 64803 69192 69956 74096 76673 77899 79803 81210 83387 87300 88324 90355 93420 94228 96495 97831 102312 102553 103417 103418 103536 113348 113349 116138 116764 116765 116849 117750 123669 123882 124804 129177 130116 130117 130387 132160 132305 133287 135581 137103 138113 139844 140675 145228 152646 153200 157616 157617 164306 170680 173681 177033 177310 177396 177547 192311 193077 199090 204265 207319 209257 210979 213040 214822 216371 217417 222989 223326 224413 224636 230598 231128 233016 237322 244822 244826 247611 249223 251942 252325] INFO 2025-06-26 13:04:30,487 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/gps.log (262508 bytes) INFO 2025-06-26 13:04:30,524 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/hydroscatlog.log (15210794 bytes) INFO 2025-06-26 13:04:32,308 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.239.05/hydroscatlog.log: [ 3 4 5 27 28 44 92 104 106 237 238 303 317 327 481 531 553 613 645 780 796 922 923 939 1070 1096 1198 1283 1382 1770 1789 1790 1865 2077 2084 2177 2188 2267 2345 2393 2677 3117 3123 3264 3341 3369 3456 3529 3910 4108 4664 4681 4874 4902 4945 5085 5099 5128 5227 5477 5960 6092 6965 7638 7772 8897 8898 9083 9092 10412 10413 10895 10939 11250 11386 11528 11578 11579 11642 13299 13568 13860 14975 16331 16332 17667 20284 20565 22341 22442 22558 22559 23054 23325 23799 24017 25467 26405 26530 26531 26589 27330 27348 27402 27775 28135 31528 33415 33742 34853 34909 35986 36497 38151 38152 38647 39598 39819 40800 40970 42419 43700 45484 45761 45762 49917 49929 49930 52873 52874 53687 56645 59395 60333 60957 61315 61341 61951 61952 62747 62748 63367 63637 64932 67109 69318 70082 70768 74223 78024 79928 81333 81334 87424 88395 88447 89488 90225 91932 93142 93540 93541 94348 94821 94932 95562 96618 96943 97952 101458 102431 102432 103657 109782 110367 113477 113478 116267 116978 116979 123421 123794 123795 124008 124683 129300 130240 130511 131122 132284 132429 133409 133410 137807 138237 139931 139970 140801 142321 143350 143947 145353 147436 150658 152466 157274 157738 159577 162429 163289 164086 164253 164428 169932 170800 170801 173241 177151 177429 177515 177666 180916 183240 184931 186970 188028 188454 190943 192893 193925 195142 197662 197663 199205 199933 202258 204378 205460 207431 208925 209369 211902 212280 215038 216485 217531 222433 223102 223103 223439 223600 224750 228758 228759 233126 234158 236115 237821 237951 243104 244932 247718 249328 252048 252431 252590 253240] INFO 2025-06-26 13:04:32,355 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/navigation.log (74672414 bytes) INFO 2025-06-26 13:04:37,690 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/isuslog.log (1504149 bytes) INFO 2025-06-26 13:04:37,839 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/parosci.log (26658758 bytes) INFO 2025-06-26 13:04:40,077 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/tailCone.log (3101227 bytes) INFO 2025-06-26 13:04:40,477 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.239.05/biolume.log (17253916 bytes) INFO 2025-06-26 13:04:42,121 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 13:04:42,992 logs2netcdfs.py download_process_logs():807 [1] Time to process: 15.92 seconds WARNING 2025-06-26 13:04:42,992 process.py download_process():196 [1] No lopc.bin file for 2007.239.05 INFO 2025-06-26 13:04:42,992 process.py calibrate():227 [1] Calibration steps for 2007.239.05 INFO 2025-06-26 13:04:43,492 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 13:04:43,494 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 13:04:44,349 calibrate.py _nudge_pos():1806 [1] 107: 0.070 0.0003254 -0.0001927 10520 35.40 1.367 -1.009 2007-08-27T21:55:47.414978048 INFO 2025-06-26 13:04:44,859 calibrate.py _nudge_pos():1806 [1] 157: 0.070 0.0007142 -0.0002433 15909 53.18 1.996 -0.848 2007-08-27T22:49:47.413022976 INFO 2025-06-26 13:04:45,512 calibrate.py _nudge_pos():1806 [1] 220: 0.070 0.0033210 0.0035254 15765 52.66 9.376 12.404 2007-08-27T23:43:29.412301056 INFO 2025-06-26 13:04:46,061 calibrate.py _nudge_pos():1806 [1] 272: 0.080 0.0007582 -0.0001781 16042 53.55 2.105 -0.616 2007-08-28T00:37:53.408701952 INFO 2025-06-26 13:04:46,621 calibrate.py _nudge_pos():1806 [1] 326: 0.080 0.0034100 0.0035405 16751 55.91 9.068 11.734 2007-08-28T01:34:41.415237376 INFO 2025-06-26 13:04:47,209 calibrate.py _nudge_pos():1806 [1] 382: 0.090 0.0008951 -0.0002027 15749 52.58 2.530 -0.714 2007-08-28T02:28:11.415337216 INFO 2025-06-26 13:04:47,821 calibrate.py _nudge_pos():1806 [1] 438: 0.090 0.0032205 0.0036401 16513 55.08 8.694 12.246 2007-08-28T03:24:11.415161600 INFO 2025-06-26 13:04:48,412 calibrate.py _nudge_pos():1806 [1] 491: 0.100 0.0008880 -0.0001960 16132 53.83 2.452 -0.675 2007-08-28T04:18:53.410329600 INFO 2025-06-26 13:04:49,143 calibrate.py _nudge_pos():1806 [1] 556: 0.100 0.0032718 0.0035742 15627 52.13 9.332 12.705 2007-08-28T05:12:05.411662592 INFO 2025-06-26 13:04:49,869 calibrate.py _nudge_pos():1806 [1] 618: 0.100 0.0008765 -0.0002018 16414 54.78 2.378 -0.683 2007-08-28T06:07:53.412308736 INFO 2025-06-26 13:04:50,472 calibrate.py _nudge_pos():1806 [1] 672: 0.110 0.0033027 0.0035034 15734 52.51 9.351 12.362 2007-08-28T07:01:17.412819712 INFO 2025-06-26 13:04:51,106 calibrate.py _nudge_pos():1806 [1] 729: 0.110 0.0009933 -0.0003174 16653 55.56 2.657 -1.058 2007-08-28T07:57:47.410588928 INFO 2025-06-26 13:04:51,807 calibrate.py _nudge_pos():1806 [1] 791: 0.110 0.0028662 0.0034930 15820 52.78 8.074 12.263 2007-08-28T08:51:35.409455872 INFO 2025-06-26 13:04:52,462 calibrate.py _nudge_pos():1806 [1] 850: 0.120 0.0010962 -0.0004794 16613 55.43 2.940 -1.603 2007-08-28T09:47:59.407636224 INFO 2025-06-26 13:04:53,144 calibrate.py _nudge_pos():1806 [1] 908: 0.120 0.0025785 0.0034499 16139 53.85 7.120 11.872 2007-08-28T10:42:47.412392448 INFO 2025-06-26 13:04:53,739 calibrate.py _nudge_pos():1806 [1] 961: 0.130 0.0011343 -0.0004848 16221 54.13 3.115 -1.659 2007-08-28T11:37:47.406327296 INFO 2025-06-26 13:04:54,286 calibrate.py _nudge_pos():1806 [1] 1010: 0.120 0.0024835 0.0034098 16657 55.60 6.642 11.364 2007-08-28T12:34:11.414507008 INFO 2025-06-26 13:04:55,082 calibrate.py _nudge_pos():1806 [1] 1080: 0.130 0.0007560 -0.0002826 15480 51.65 2.176 -1.014 2007-08-28T13:26:59.407484416 INFO 2025-06-26 13:04:55,653 calibrate.py _nudge_pos():1806 [1] 1130: 0.130 0.0021851 0.0028192 13785 45.98 7.065 11.361 2007-08-28T14:13:47.415122688 INFO 2025-06-26 13:05:24,895 calibrate.py _nudge_pos():1862 [1] 3603: - - - 2 0.00 - - INFO 2025-06-26 13:05:24,896 calibrate.py _nudge_pos():1868 [1] Points in final series = 316400 WARNING 2025-06-26 13:05:25,317 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 13:05:59,013 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:06:17,178 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:06:19,114 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:06:19,118 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.239.05/ctd1.nc INFO 2025-06-26 13:06:19,120 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 13:06:19,120 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 13:06:19,120 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 13:06:33,134 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:06:35,052 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 13:06:35,057 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.239.05/ctd2.nc INFO 2025-06-26 13:06:35,058 calibrate.py _range_qc_combined_nc():898 [1] Setting 170 ctd2_salinity values to NaN INFO 2025-06-26 13:06:35,059 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 13:06:35,059 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 13:06:35,149 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 13:06:38,141 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3789382 3801540 3801541] INFO 2025-06-26 13:06:38,696 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 13:06:38,703 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 13:06:38,703 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.239.05 ERROR 2025-06-26 13:06:38,703 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.239.05 INFO 2025-06-26 13:06:38,763 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_cal.nc INFO 2025-06-26 13:06:58,456 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 13:06:58,461 process.py align():251 [1] Alignment steps for 2007.239.05 INFO 2025-06-26 13:06:58,500 align.py process_cal():139 [1] Processing dorado_2007.239.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.239.05 INFO 2025-06-26 13:06:58,581 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:06:58,589 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:06:58,793 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:06:58,805 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:06:58,999 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:06:59,011 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:06:59,129 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 13:06:59,129 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 13:06:59,212 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 13:06:59,223 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 13:06:59,415 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:06:59,425 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:06:59,593 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:06:59,602 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:06:59,771 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:06:59,780 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 13:06:59,947 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:06:59,957 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:00,133 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:00,143 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:00,311 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:00,320 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:00,490 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:00,499 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:00,666 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:00,675 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:00,846 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:00,855 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:01,024 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:01,034 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:01,206 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:01,216 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:01,384 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:01,393 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:01,561 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:01,569 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:01,743 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:01,752 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:01,921 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:01,931 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:02,104 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:02,116 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:02,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:02,297 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:02,474 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:02,484 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:02,656 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:02,666 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:02,837 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.239.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 13:07:02,845 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 13:07:03,054 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.74 INFO 2025-06-26 13:07:03,182 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.74 INFO 2025-06-26 13:07:03,316 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.74 INFO 2025-06-26 13:07:03,451 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 13:07:03,589 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 13:07:03,628 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_align.nc INFO 2025-06-26 13:07:03,762 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 13:07:03,765 process.py resample():273 [1] Resampling steps for 2007.239.05 INFO 2025-06-26 13:07:03,765 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 13:07:03,798 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_align.nc mission netCDF file INFO 2025-06-26 13:07:03,806 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_align.nc mission netCDF file INFO 2025-06-26 13:07:03,808 resample.py get_mission_start_end():1145 [1] navigation: 2007-08-27T21:19:09.785526016 to 2007-08-28T14:55:30.813628160 (0 days 00:00:00 before mission_end) INFO 2025-06-26 13:07:03,811 resample.py get_mission_start_end():1145 [1] hs2 : 2007-08-27T21:18:43.797306368 to 2007-08-28T14:55:30.753632256 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 13:07:03,813 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-08-27T21:19:04.725872640 to 2007-08-28T14:55:30.623641344 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 13:07:03,816 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-08-27T21:19:04.845864192 to 2007-08-28T14:55:30.613641984 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 13:07:03,817 resample.py get_mission_start_end():1145 [1] isus : 2007-08-27T21:20:11.231316736 to 2007-08-28T14:55:29.873692416 (0 days 00:00:00.939935744 before mission_end) INFO 2025-06-26 13:07:03,819 resample.py get_mission_start_end():1145 [1] biolume : 2007-08-27T21:18:35.767822080 to 2007-08-28T14:55:29.973651456 (0 days 00:00:00.839976704 before mission_end) INFO 2025-06-26 13:07:03,821 resample.py get_mission_start_end():1145 [1] tailcone : 2007-08-27T21:18:40.477533696 to 2007-08-28T14:55:30.563645440 (0 days 00:00:00.249982720 before mission_end) INFO 2025-06-26 13:07:03,821 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_align.nc mission netCDF file INFO 2025-06-26 13:07:03,822 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:04,463 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:04,565 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:04,664 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:04,764 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:04,851 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:04,971 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,071 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,154 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,234 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,314 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,393 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,471 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,552 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,631 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,711 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,789 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,871 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:05,951 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,037 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,120 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,200 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,279 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,310 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,339 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,365 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,397 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,429 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 13:07:06,878 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_1S.nc INFO 2025-06-26 13:07:09,994 create_products.py gulper_odv():401 [1] No gulper times found for 2007.239.05 INFO 2025-06-26 13:07:09,994 process.py archive():337 [1] Archiving steps for 2007.239.05 INFO 2025-06-26 13:07:09,994 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05, BASE_PATH = /data/auv_data INFO 2025-06-26 13:07:09,996 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 13:07:09,998 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.239.05_1S.nc INFO 2025-06-26 13:07:10,044 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:07:10,045 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.239.05_cal.nc INFO 2025-06-26 13:07:10,271 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:07:10,272 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.239.05_align.nc INFO 2025-06-26 13:07:10,472 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 13:07:10,534 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,597 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,603 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,648 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,832 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,841 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,911 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:10,926 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:11,074 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007239/2007.239.05 done. INFO 2025-06-26 13:07:11,075 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 13:07:11,075 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.239.05/dorado_2007.239.05_processing.log /Volumes/AUVCTD/surveys/2007/netcdf