INFO 2025-06-26 12:37:20,214 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 12:37:20,214 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 12:37:20,214 process.py process_mission():449 [1] Processing AUVCTD mission 2007.134.04 by user docker_user on host eae60d30a712 INFO 2025-06-26 12:37:20,214 process.py download_process():165 [1] Download and processing steps for 2007.134.04 INFO 2025-06-26 12:37:20,215 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2007/2007134/2007.134.04 INFO 2025-06-26 12:37:20,215 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2007/2007134/2007.134.04 to /data/auv_data/dorado/missionlogs/2007.134.04 INFO 2025-06-26 12:37:21,226 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2007.134.04 INFO 2025-06-26 12:37:21,226 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/ctdDriver.log (548195 bytes) INFO 2025-06-26 12:37:21,271 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.04/ctdDriver.log: [ 8 142 233 239 244 322 384 448 472 564 742 754 981 990 1021 1037 1048 1199 1496 1789 2113 2122 2239 2300 2340 3201 3357 3428 3538 3655 3661 4183 4190 5007 5350 5405 5539] INFO 2025-06-26 12:37:21,273 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/ctdDriver2.log (546957 bytes) INFO 2025-06-26 12:37:21,316 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.04/ctdDriver2.log: [ 3 138 229 235 240 317 380 444 467 738 750 977 986 1017 1033 1194 1576 1583 1785 2110 2296 2335 3415 3526 3643 3649 4170 4176 4826 4992 4999 5107 5335 5390 5512 5524] INFO 2025-06-26 12:37:21,318 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/gps.log (8708 bytes) INFO 2025-06-26 12:37:21,327 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/hydroscatlog.log (379094 bytes) INFO 2025-06-26 12:37:21,379 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2007.134.04/hydroscatlog.log: [ 3 5 8 84 95 217 308 314 319 459 523 633 817 828 1055 1056 1065 1096 1108 1531 1616 1660 1697 1861 2196 2310 2374 2414 2491 2850 3618 3741 4269 4919 4920 5096 5328 5417 5431 5486 5620] INFO 2025-06-26 12:37:21,380 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/navigation.log (1817090 bytes) INFO 2025-06-26 12:37:21,526 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/isuslog.log (34581 bytes) INFO 2025-06-26 12:37:21,533 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/parosci.log (656630 bytes) INFO 2025-06-26 12:37:21,604 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/tailCone.log (77371 bytes) INFO 2025-06-26 12:37:21,620 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2007.134.04/biolume.log (434524 bytes) INFO 2025-06-26 12:37:21,665 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 12:37:21,691 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.46 seconds WARNING 2025-06-26 12:37:21,691 process.py download_process():196 [1] No lopc.bin file for 2007.134.04 INFO 2025-06-26 12:37:21,691 process.py calibrate():227 [1] Calibration steps for 2007.134.04 INFO 2025-06-26 12:37:21,759 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 12:37:21,761 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 12:37:22,268 calibrate.py _nudge_pos():1806 [1] 82: 0.460 0.0001030 -0.0000156 45 0.15 104.370 -19.767 2007-05-14T16:50:30.045259776 INFO 2025-06-26 12:37:22,306 calibrate.py _nudge_pos():1806 [1] 86: 0.130 -0.0016678 0.0001473 7299 24.55 -10.094 1.112 2007-05-14T17:15:06.044146688 INFO 2025-06-26 12:37:22,514 calibrate.py _nudge_pos():1862 [1] 74: - - - 1 0.00 - - INFO 2025-06-26 12:37:22,514 calibrate.py _nudge_pos():1868 [1] Points in final series = 7691 WARNING 2025-06-26 12:37:22,529 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 12:37:23,382 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:37:23,839 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:37:23,888 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 12:37:23,889 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2007.134.04/ctd1.nc INFO 2025-06-26 12:37:23,891 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 12:37:23,891 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 12:37:23,891 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 12:37:24,248 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:37:24,299 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 12:37:24,301 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2007.134.04/ctd2.nc INFO 2025-06-26 12:37:24,302 calibrate.py _range_qc_combined_nc():898 [1] Setting 174 ctd2_salinity values to NaN INFO 2025-06-26 12:37:24,303 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 12:37:24,303 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 12:37:24,314 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 12:37:24,383 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 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 660 661 662 663 664 665 666 667 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1860 1861 1862 1863 1864 1865 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2100 2101 2102 2103 2104 5400 5401 5402 5403 5404 5405 5406 5407 5408 5409 5410 5411 5412 5413 5414 5415 5416 7500 7501 7502 7503 7504 7505 7506 7507 7508 7509 7510 7511 7512 7513 7514 8460 8461 8462 8463 8464 8465 8466 8467 8468 8469 8470 8471 8472 8473 8474 8475 8476 8477 8820 8821 8822 8823 8824 8825 10200 10201 10202 10203 10204 10205 10206 10207 10208 10209 10210 17460 17461 17462 17463 17464 17465 17466 17467 17468 17469 17470 17471 24180 24181 24182 24183 24184 24185 24186 24187 24188 24189 24190 24191 24720 24721 24722 24723 24724 24725 24900 24901 24902 24903 24904 24905 24906 24907 25440 25441 25442 25443 25444 25445 25446 25447 25448 25449 25450 25451 25452 25453 25454 25455 25560 25561 25562 25563 25564 25565 25566 25567 25568 25569 26100 26101 26102 26103 26104 26105 26106 26107 26108 26109 26110 26111 26112 26113 26114 26115 26116 26117 26118 26119 26120 33480 33600 33601 33602 33603 33604 33605 33606 33607 33608 33609 33610 33611 33612 33613 34380 34381 34382 34383 34384 34385 34386 34387 34388 34389 34390 34391 34392 34393 34394 34395 34396 34397 34398 34399 34400 35340 35341 35342 35343 35344 35345 35346 35347 35348 35349 35350 35351 37800 37801 37802 37803 37804 37805 37806 37807 37808 37809 37810 37811 37812 37813 37814 37815 37816 37817 37818 37819 37820 37980 37981 37982 37983 37984 37985 37986 37987 37988 37989 37990 37991 37992 37993 37994 37995 37996 37997 37998 37999 38000 38001 38520 38521 38522 38523 38524 38525 38526 38527 38528 38529 38530 38531 38532 38533 38534 38535 38536 38537 49860 49861 49862 49863 50460 50461 50462 50463 50464 50465 50466 50467 50468 50469 52020 52021 52022 52023 52024 52025 52026 52027 52028 52200 52201 52202 52203 52204 52205 52206 52207 52208 52209 52210 52211 52212 52213 52214 56760 56761 56762 56763 56764 56765 56766 56767 56768 56769 56770 56771 56772 56773 56774 56775 56776 56777 56778 56779 56780 56781 74460 74461 74462 74463 74464 74465 74466 74467 74468 74469 74470 74471 74472 74473 74474 74475 74476 74477 74478 76980 76981 76982 76983 76984 76985 76986 76987 76988 76989 76990 76991 76992 76993 76994 76995 76996 76997 76998 77100 77101 77102 77103 77104 77105 77106 77107 77108 77109 77110 77111 77112 78720 78721 82140 82141 82142 82143 82144 82145 82146 82147 82148 82149 82150 82151 82152 82153 82154 84780 84781 84782 84783 84784 84785 84786 84787 84788 84789 84790 84791 84792 84793 84794 84795 84796 84797 84798 84799 84800 84801 84802 84803 84804] INFO 2025-06-26 12:37:24,400 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 12:37:24,405 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 12:37:24,406 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.134.04 ERROR 2025-06-26 12:37:24,406 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.134.04 INFO 2025-06-26 12:37:24,410 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_cal.nc INFO 2025-06-26 12:37:24,939 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 12:37:24,943 process.py align():251 [1] Alignment steps for 2007.134.04 INFO 2025-06-26 12:37:24,965 align.py process_cal():139 [1] Processing dorado_2007.134.04_cal.nc from /data/auv_data/dorado/missionnetcdfs/2007.134.04 INFO 2025-06-26 12:37:24,972 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:24,973 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 12:37:24,987 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:24,989 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 12:37:25,001 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:25,003 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 12:37:25,012 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 12:37:25,012 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 12:37:25,017 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 12:37:25,019 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.95 INFO 2025-06-26 12:37:25,032 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,034 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,046 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,048 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,060 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,062 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,074 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,076 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,088 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,090 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,103 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,105 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,117 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,119 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,132 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,134 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,146 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,148 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,161 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,163 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,175 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,178 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,190 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,192 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,204 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,206 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 3.97 INFO 2025-06-26 12:37:25,219 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,221 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,234 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,236 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,249 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,251 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,264 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,266 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,279 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,281 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,294 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,296 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,309 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.134.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 12:37:25,311 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 3.96 INFO 2025-06-26 12:37:25,327 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:37:25,342 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:37:25,356 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.71 INFO 2025-06-26 12:37:25,372 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 12:37:25,388 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.01 INFO 2025-06-26 12:37:25,399 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_align.nc INFO 2025-06-26 12:37:25,454 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 12:37:25,456 process.py resample():273 [1] Resampling steps for 2007.134.04 INFO 2025-06-26 12:37:25,457 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 12:37:25,479 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_align.nc mission netCDF file INFO 2025-06-26 12:37:25,484 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_align.nc mission netCDF file INFO 2025-06-26 12:37:25,485 resample.py get_mission_start_end():1145 [1] navigation: 2007-05-14T16:49:36.008961536 to 2007-05-14T17:15:28.242626304 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 12:37:25,486 resample.py get_mission_start_end():1145 [1] hs2 : 2007-05-14T16:49:12.030604032 to 2007-05-14T17:15:28.182630400 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 12:37:25,488 resample.py get_mission_start_end():1145 [1] ctd1 : 2007-05-14T16:49:30.539336192 to 2007-05-14T17:15:28.242626304 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 12:37:25,489 resample.py get_mission_start_end():1145 [1] ctd2 : 2007-05-14T16:49:31.139294976 to 2007-05-14T17:15:28.342619392 (0 days 00:00:00 before mission_end) INFO 2025-06-26 12:37:25,490 resample.py get_mission_start_end():1145 [1] isus : 2007-05-14T16:50:16.846163968 to 2007-05-14T17:15:27.652666624 (0 days 00:00:00.689952768 before mission_end) INFO 2025-06-26 12:37:25,492 resample.py get_mission_start_end():1145 [1] biolume : 2007-05-14T16:49:03.781135104 to 2007-05-14T17:15:27.762624768 (0 days 00:00:00.579994624 before mission_end) INFO 2025-06-26 12:37:25,493 resample.py get_mission_start_end():1145 [1] tailcone : 2007-05-14T16:49:02.481258496 to 2007-05-14T17:15:27.972644608 (0 days 00:00:00.369974784 before mission_end) INFO 2025-06-26 12:37:25,494 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_align.nc mission netCDF file INFO 2025-06-26 12:37:25,494 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,538 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,549 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,559 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,569 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,579 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,589 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,598 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,608 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,616 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,626 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,638 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,648 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,658 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,667 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,675 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,683 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,693 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,702 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,712 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,721 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,730 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,739 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,748 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,756 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,764 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,774 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,783 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 12:37:25,882 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_1S.nc INFO 2025-06-26 12:37:26,964 create_products.py gulper_odv():401 [1] No gulper times found for 2007.134.04 INFO 2025-06-26 12:37:26,964 process.py archive():337 [1] Archiving steps for 2007.134.04 INFO 2025-06-26 12:37:26,964 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04, BASE_PATH = /data/auv_data INFO 2025-06-26 12:37:26,964 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2025-06-26 12:37:26,965 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.04_1S.nc INFO 2025-06-26 12:37:26,973 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:37:26,974 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.04_cal.nc INFO 2025-06-26 12:37:26,987 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:37:26,988 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2007/netcdf/dorado_2007.134.04_align.nc INFO 2025-06-26 12:37:27,000 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2025-06-26 12:37:27,009 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,017 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,020 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,026 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,036 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,040 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,048 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,052 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,062 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007134/2007.134.04 done. INFO 2025-06-26 12:37:27,063 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 12:37:27,063 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2007.134.04/dorado_2007.134.04_processing.log /Volumes/AUVCTD/surveys/2007/netcdf