INFO 2025-06-26 12:37:27,072 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 12:37:27,072 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD missions - Bellingham looking for internal waves in Southern MB - ctdToUse = ctd1 INFO 2025-06-26 12:37:27,072 process.py process_mission():449 [1] Processing AUVCTD mission 2007.134.06 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:37:27,072 process.py download_process():165 [1] Download and processing steps for 2007.134.06 INFO 2025-06-26 12:37:27,072 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007134/2007.134.06 INFO 2025-06-26 12:37:27,073 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007134/2007.134.06 to /data/auv_data/dorado/missionlogs/2007.134.06 INFO 2025-06-26 12:37:28,134 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.134.06 INFO 2025-06-26 12:37:28,134 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/ctdDriver.log (669811 bytes) INFO 2025-06-26 12:37:28,187 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.06/ctdDriver.log: [ 3 23 231 239 389 441 631 689 1337 1534 1536 1619 1825 1833 2216 2235 2292 2395 2397 2771 3019 3310 3344 3426 3676 4243 4676 4828 4948 5017 5356 5587 7155 7286] INFO 2025-06-26 12:37:28,189 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/ctdDriver2.log (669629 bytes) INFO 2025-06-26 12:37:28,242 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.06/ctdDriver2.log: [ 22 230 239 388 440 688 1336 1532 1534 1616 1823 1831 2041 2214 2231 2289 2391 2394 2767 3016 3187 3307 3421 3672 4126 4180 4238 4672 4824 5014 5341 5352 5584 6218 7152 7283] INFO 2025-06-26 12:37:28,244 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/gps.log (10076 bytes) INFO 2025-06-26 12:37:28,252 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/hydroscatlog.log (462614 bytes) INFO 2025-06-26 12:37:28,313 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.06/hydroscatlog.log: [ 4 8 32 42 90 92 109 294 318 529 641 648 720 743 777 840 1062 1087 1286 1427 1524 1574 1581 1627 1924 2133 2306 2323 2325 2487 3280 3434 3435 3516 3637 3767 4333 4766 5005 5038 5211 5325 5436 6390 6504 7244 7598] INFO 2025-06-26 12:37:28,315 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/navigation.log (2225842 bytes) INFO 2025-06-26 12:37:28,489 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/isuslog.log (43061 bytes) INFO 2025-06-26 12:37:28,498 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.06/isuslog.log: [1 2 3 4 5 6 8] INFO 2025-06-26 12:37:28,498 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/parosci.log (801350 bytes) INFO 2025-06-26 12:37:28,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/tailCone.log (94123 bytes) INFO 2025-06-26 12:37:28,588 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.06/biolume.log (528636 bytes) INFO 2025-06-26 12:37:28,640 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:37:28,671 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.54 seconds WARNING 2025-06-26 12:37:28,671 process.py download_process():196 [1] No lopc.bin file for 2007.134.06 INFO 2025-06-26 12:37:28,671 process.py calibrate():227 [1] Calibration steps for 2007.134.06 INFO 2025-06-26 12:37:28,737 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 12:37:28,739 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:37:29,440 calibrate.py _nudge_pos():1806 [1] 102: 0.190 -0.0017232 -0.0013273 8952 30.05 -8.521 -8.185 2007-05-14T18:24:29.978897920 INFO 2025-06-26 12:37:29,678 calibrate.py _nudge_pos():1862 [1] 96: - - - 2 0.00 - - INFO 2025-06-26 12:37:29,678 calibrate.py _nudge_pos():1868 [1] Points in final series = 9422 WARNING 2025-06-26 12:37:29,695 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 12:37:30,734 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:37:31,295 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:37:31,355 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 22 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:37:31,356 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.134.06/ctd1.nc INFO 2025-06-26 12:37:31,357 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 12:37:31,357 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 12:37:31,357 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:37:31,795 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:37:31,855 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 22 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:37:31,857 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.134.06/ctd2.nc INFO 2025-06-26 12:37:31,858 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 12:37:31,858 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 12:37:31,858 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:37:31,929 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:37:32,012 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 4020 4021 4022 4023 5280 5281 5282 5283 5284 5285 5286 5287 5288 5289 5290 5291 5292 5293 5294 5295 5296 5297 5400 5401 5402 5403 5404 5405 5406 5407 5408 5409 5410 5411 5412 5413 5414 5415 5416 5417 5418 5419 5420 5421 5422 5423 11280 11281 11282 11283 11284 11285 11286 11287 11288 11289 11290 11291 11292 11293 11294 11295 11296 11297 11298 11299 11300 11640 11641 11642 11643 11644 11645 11646 11647 11648 11649 11650 11651 11652 13080 13081 13082 13083 13084 13085 13086 13087 13088 13089 13090 13091 13092 13093 13094 13095 13096 13097 13098 13099 13100 13101 13102 13103 13104 13105 13106 13107 16440 16441 16800 16801 16802 16803 16804 16805 16806 16807 16808 16809 16810 16811 16812 16813 16814 16815 16816 16817 16818 16920 16921 16922 16923 16924 16925 16926 16927 16928 16929 16930 16931 16932 16933 16934 16935 16936 16937 16938 16939 16940 17280 17281 17282 17283 17284 17285 17286 17287 17288 17289 17290 17291 17292 19800 21900 21901 21902 21903 21904 21905 21906 24180 24181 24182 24183 24184 24185 24186 24187 24188 24189 24190 24191 24192 24193 24194 24195 24196 24900 24901 24902 24903 24904 24905 24906 24907 24908 24909 24910 24911 29220 29221 29222 29223 29224 29225 29226 29227 29228 29229 29230 29231 29232 29233 29234 29235 29236 29237 29238 29239 29240 29241 29242 29243 29244 29245 29340 29341 29342 29343 29344 29345 29346 29347 29348 29349 29350 29351 29352 29353 29354 29355 29356 29357 29358 29359 29360 29361 29362 29363 29364 32520 32521 35100 35101 35102 35103 35104 35105 35106 35107 35108 35109 35110 35111 35112 35113 35114 35115 36240 36241 36242 36243 36244 36245 36246 36247 36248 36249 36250 36251 36252 36253 36254 36255 48300 48301 48302 48303 48304 48305 48306 48307 48308 48309 48310 48311 48312 48313 48314 48315 48316 48317 48318 52020 52021 52022 52023 55080 55081 65520 65521 65522 65523 65524 65525 65526 65527 65528 72000 72001 72002 72003 72004 72005 72006 72007 72008 72009 72010 72011 72012 72013 72014 72015 72016 72017 72018 72019 72020 72021 72022 72023 72024 72025 72026 72027 75600 75601 75602 76080 76081 76082 76083 76084 76085 76086 76087 76088 76089 76090 76091 76092 76093 76094 76095 76096 76097 76098 76099 76100 76101 76980 76981 76982 76983 76984 76985 76986 76987 76988 76989 76990 76991 76992 76993 76994 76995 76996 76997 76998 76999 77000 77001 77520 77521 77522 77523 77524 77525 77526 77527 77528 77529 77530 77531 77532 77533 77534 77535 77536 77537 77538 77539 77540 77541 77542 77543 77544 80400 80401 80402 80403 95220 95221 111180 111181 111182 111183 111184 111185 111186 111187 111188 111189 111190 111191 111192 111193 111194 111195 111196 111197 111198 112860 112861 112862 112863 112864 112865 112866 112867 112868 112869 112870 112871 112872 112873 112874 112875 112876 112877 112878 112879 112880 112881 112882 112883 112884 114660 114661 114662 114663 114664 114665 114666 114667 114668 114669 114670 114671 114672 114673 114674 114675] INFO 2025-06-26 12:37:32,034 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -7 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 12:37:32,039 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 12:37:32,039 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.134.06 ERROR 2025-06-26 12:37:32,039 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.134.06 INFO 2025-06-26 12:37:32,044 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_cal.nc INFO 2025-06-26 12:37:32,675 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 12:37:32,679 process.py align():251 [1] Alignment steps for 2007.134.06 INFO 2025-06-26 12:37:32,701 align.py process_cal():139 [1] Processing dorado_2007.134.06_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.134.06 INFO 2025-06-26 12:37:32,707 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:32,709 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:37:32,724 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:32,726 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:37:32,739 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:32,741 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:37:32,749 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:37:32,749 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:37:32,754 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:32,756 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.97 INFO 2025-06-26 12:37:32,770 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,771 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:32,784 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,786 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:32,800 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,802 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:32,815 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,817 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,830 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,832 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,847 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,860 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,862 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,876 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,878 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,891 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,893 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,907 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,909 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,922 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,924 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,937 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,939 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,952 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,954 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.98 INFO 2025-06-26 12:37:32,968 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,970 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:32,985 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:32,987 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:33,002 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:33,004 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:33,018 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:33,021 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:33,035 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:33,037 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:33,051 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:33,053 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:33,067 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:33,069 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:33,087 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:37:33,102 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:37:33,118 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:37:33,134 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:37:33,151 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 12:37:33,161 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_align.nc INFO 2025-06-26 12:37:33,208 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 12:37:33,210 process.py resample():273 [1] Resampling steps for 2007.134.06 INFO 2025-06-26 12:37:33,211 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:37:33,232 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_align.nc mission netCDF file INFO 2025-06-26 12:37:33,237 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_align.nc mission netCDF file INFO 2025-06-26 12:37:33,238 resample.py get_mission_start_end():1145 [1] navigation: 2007-05-14T17:53:18.547099648 to 2007-05-14T18:24:55.987116032 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 12:37:33,239 resample.py get_mission_start_end():1145 [1] hs2 : 2007-05-14T17:52:51.588946432 to 2007-05-14T18:24:55.897122304 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 12:37:33,241 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-05-14T17:53:12.787494144 to 2007-05-14T18:24:55.977116928 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 12:37:33,242 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-05-14T17:53:12.877488128 to 2007-05-14T18:24:56.067110656 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:37:33,243 resample.py get_mission_start_end():1145 [1] isus : 2007-05-14T17:53:44.595315200 to 2007-05-14T18:24:55.577144064 (0 days 00:00:00.489966592 before mission_end) INFO 2025-06-26 12:37:33,244 resample.py get_mission_start_end():1145 [1] biolume : 2007-05-14T17:52:44.209417728 to 2007-05-14T18:24:55.547111936 (0 days 00:00:00.519998720 before mission_end) INFO 2025-06-26 12:37:33,246 resample.py get_mission_start_end():1145 [1] tailcone : 2007-05-14T17:52:49.749072640 to 2007-05-14T18:24:55.837126400 (0 days 00:00:00.229984256 before mission_end) INFO 2025-06-26 12:37:33,246 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_align.nc mission netCDF file INFO 2025-06-26 12:37:33,247 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,294 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,305 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,316 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,326 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,337 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,347 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,357 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,367 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,376 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,385 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,393 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,402 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,411 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,419 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,428 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,437 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,447 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,457 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,466 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,476 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,486 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,495 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,504 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,512 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,521 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,530 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,539 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:33,643 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_1S.nc INFO 2025-06-26 12:37:34,759 create_products.py gulper_odv():401 [1] No gulper times found for 2007.134.06 INFO 2025-06-26 12:37:34,759 process.py archive():337 [1] Archiving steps for 2007.134.06 INFO 2025-06-26 12:37:34,759 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06, BASE_PATH = /data/auv_data INFO 2025-06-26 12:37:34,759 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:37:34,761 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.06_1S.nc INFO 2025-06-26 12:37:34,770 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:37:34,771 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.06_cal.nc INFO 2025-06-26 12:37:34,785 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:37:34,786 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.06_align.nc INFO 2025-06-26 12:37:34,798 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:37:34,807 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,814 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,818 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,824 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,835 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,839 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,846 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,850 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,861 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.06 done. INFO 2025-06-26 12:37:34,861 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:37:34,861 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.06/dorado_2007.134.06_processing.log /Volumes/AUVCTD/surveys/2007/netcdf