INFO 2025-06-26 16:25:38,524 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 16:25:38,525 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey fourth day-time one for BloomEx in October 2010 - ctdToUse = ctd1 INFO 2025-06-26 16:25:38,525 process.py process_mission():449 [1] Processing AUVCTD mission 2010.280.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:25:38,525 process.py download_process():165 [1] Download and processing steps for 2010.280.01 INFO 2025-06-26 16:25:38,525 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010280/2010.280.01 INFO 2025-06-26 16:25:38,525 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010280/2010.280.01 to /data/auv_data/dorado/missionlogs/2010.280.01 INFO 2025-06-26 16:25:41,755 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.280.01 INFO 2025-06-26 16:25:41,755 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/ctdDriver.log (4555499 bytes) INFO 2025-06-26 16:25:42,153 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.280.01/ctdDriver.log: [ 726 2236 2441 3369 3526 3716 4886 5067 6227 6517 7906 8377 10117 10936 11411 12567 14276 17197 17934 20010 22923 24142 25424 26006 26214 28502 30500 34861 36267 37035 40447 40571] INFO 2025-06-26 16:25:42,171 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/ctdDriver2.log (4568063 bytes) INFO 2025-06-26 16:25:42,518 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.280.01/ctdDriver2.log: [ 90 518 701 857 2260 2572 3500 3657 4300 5017 5198 6358 6648 8037 11067 11542 12698 17328 18065 20141 23083 24273 25555 26138 27492 28633 30631 36398 37166 40578 40702 42301 45039] INFO 2025-06-26 16:25:42,546 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/gps.log (72860 bytes) INFO 2025-06-26 16:25:42,563 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/hydroscatlog.log (4002706 bytes) INFO 2025-06-26 16:25:42,996 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.280.01/hydroscatlog.log: [ 78 343 381 455 594 747 1563 1573 1661 1667 1732 2232 4029 4798 5191 5479 5601 5792 6593 7767 8385 9555 11825 14473 17402 21951 23471 24875 25847 26416 28452 28755 31496 37231 38828 40766] INFO 2025-06-26 16:25:43,015 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/navigation.log (13980058 bytes) INFO 2025-06-26 16:25:44,151 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/isuslog.log (295445 bytes) INFO 2025-06-26 16:25:44,184 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.280.01/isuslog.log: [ 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 19] INFO 2025-06-26 16:25:44,186 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/parosci.log (5216726 bytes) INFO 2025-06-26 16:25:44,696 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/tailCone.log (2849563 bytes) INFO 2025-06-26 16:25:45,059 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/biolume.log (3332310 bytes) INFO 2025-06-26 16:25:45,401 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:25:45,602 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.85 seconds INFO 2025-06-26 16:25:45,603 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.280.01/lopc.bin (44904000 bytes) INFO 2025-06-26 16:25:45,603 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:25:45 2025 INFO 2025-06-26 16:25:45,603 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.280.01/parosci.nc INFO 2025-06-26 16:25:45,603 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:25:45,603 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.280.01/parosci.nc INFO 2025-06-26 16:25:45,608 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1286476554.7, sensor_off_time = 1286488475.2 INFO 2025-06-26 16:25:45,608 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11920 seconds. Expecting to read 23840 L frames from the lopc.bin file. INFO 2025-06-26 16:25:45,608 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 23840 records from the lopc.bin file. INFO 2025-06-26 16:25:45,751 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-07 18:35:54 Z and endTime = 2010-10-07 21:54:35 Z with 23840 records expected to be read from lopc.bin INFO 2025-06-26 16:25:45,751 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.280.01/lopc.bin INFO 2025-06-26 16:25:45,751 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.280.01/lopc.nc INFO 2025-06-26 16:25:45,751 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.280.01/lopc.nc INFO 2025-06-26 16:25:45,752 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.280.01 INFO 2025-06-26 16:25:45,752 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 16:25:45,756 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0163314 WARNING 2025-06-26 16:25:45,756 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 16:25:45,819 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:25:45,819 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:25:45,819 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:25:46,069 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 16:25:46,070 process.py calibrate():227 [1] Calibration steps for 2010.280.01 INFO 2025-06-26 16:25:46,224 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 16:25:46,226 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:25:47,047 calibrate.py _nudge_pos():1806 [1] 126: 0.140 -0.0003795 -0.0003265 1366 4.63 -12.145 -13.069 2010-10-07T18:42:35.019729920 INFO 2025-06-26 16:25:47,565 calibrate.py _nudge_pos():1806 [1] 180: 0.140 0.0017763 -0.0006679 6183 20.71 12.704 -5.975 2010-10-07T19:04:11.020947712 INFO 2025-06-26 16:25:47,594 calibrate.py _nudge_pos():1806 [1] 183: 0.150 0.0000004 -0.0000147 65 0.21 0.305 -12.740 2010-10-07T19:04:26.019920384 INFO 2025-06-26 16:25:48,230 calibrate.py _nudge_pos():1806 [1] 250: 0.150 -0.0002377 -0.0000087 2257 7.55 -4.665 -0.215 2010-10-07T19:13:05.014366720 INFO 2025-06-26 16:25:48,960 calibrate.py _nudge_pos():1806 [1] 326: 0.140 -0.0032696 -0.0067258 7740 25.85 -18.737 -48.218 2010-10-07T19:40:11.022977536 INFO 2025-06-26 16:25:48,981 calibrate.py _nudge_pos():1806 [1] 328: 0.140 -0.0000228 -0.0000208 80 0.26 -12.816 -14.640 2010-10-07T19:40:28.021812992 INFO 2025-06-26 16:25:49,740 calibrate.py _nudge_pos():1806 [1] 406: 0.150 -0.0044405 -0.0045233 7862 26.23 -25.071 -31.955 2010-10-07T20:07:59.018712064 INFO 2025-06-26 16:25:50,565 calibrate.py _nudge_pos():1806 [1] 493: 0.150 0.0009255 -0.0008089 2686 8.96 15.290 -16.723 2010-10-07T20:18:23.015965184 INFO 2025-06-26 16:25:51,812 calibrate.py _nudge_pos():1806 [1] 621: 0.150 0.0060760 -0.0015817 7729 25.78 34.910 -11.369 2010-10-07T20:46:17.021287936 INFO 2025-06-26 16:25:53,485 calibrate.py _nudge_pos():1806 [1] 778: 0.150 -0.0001737 -0.0011896 2905 9.70 -2.653 -22.732 2010-10-07T20:58:35.020731648 INFO 2025-06-26 16:25:54,326 calibrate.py _nudge_pos():1806 [1] 859: 0.160 -0.0009793 -0.0018772 7959 26.56 -5.461 -13.095 2010-10-07T21:26:29.016055040 INFO 2025-06-26 16:25:55,126 calibrate.py _nudge_pos():1806 [1] 939: 0.160 -0.0011363 -0.0019121 7728 25.78 -6.530 -13.744 2010-10-07T21:53:35.014666496 INFO 2025-06-26 16:25:55,747 calibrate.py _nudge_pos():1862 [1] 949: - - - 1 0.00 - - INFO 2025-06-26 16:25:55,747 calibrate.py _nudge_pos():1868 [1] Points in final series = 59225 WARNING 2025-06-26 16:25:55,837 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:26:01,935 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 6 of 47603 INFO 2025-06-26 16:26:02,311 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 16:26:05,783 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 58 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:26:06,142 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 58 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:26:06,144 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.280.01/ctd1.nc INFO 2025-06-26 16:26:06,145 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 16:26:06,146 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 16:26:06,146 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:26:08,819 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:26:09,220 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:26:09,222 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.280.01/ctd2.nc INFO 2025-06-26 16:26:09,223 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 16:26:09,224 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 16:26:09,224 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:26:09,682 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:26:10,214 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 120 121 122 123 240 241 242 243 244 245 246 247 248 249 250 251 252 420 421 422 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069 3070 3071 3072 3073 3074 3075 3076 3077 3078 3079 3080 3081 3082 3083 4020 4021 4022 4023 4024 4025 4026 4027 4028 6180 6181 6182 7260 7261 7262 7263 7264 7265 7266 7267 7268 7269 7270 7271 9300 9301 9302 9303 9304 9305 9306 9307 9308 9309 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78421 78422 78423 78424 78425 78426 78427 78428 78429 78430 93120 93121 93122 93123 93124 93125 95520 95521 95522 95523 95524 95525 95526 95527 95528 95529 95530 95531 95532 95533 95534 95535 95536 95537 95538 95539 115140 115141 115142 115143 115144 115145 115146 117180 117181 117182 117183 117184 117185 117186 117187 117188 117189 117190 118440 120300 120301 120302 120303 120304 120305 141540 143040 143041 143042 143043 143044 143045 143046 143047 143048 143049 143050 159600 159601 159602 159603 159604 159605 159606 159607 159608 159609 159610 159611 159612 159613 159614 159615 159616 175020 175021 175022 175023 175024 175025 175026 175027 175028 176460 176461 176462 176463 176464 176465 176466 176467 176468 176469 176470 176471 176472 176473 176474 176475 176476 176477 176478 176479 176480 176481 176482 176483 176484 185880 185881 185882 185883 185884 185885 185886 214080 214081 214082 214083 214084 214085 214086 214087 214088 214089 214090 214091 214092 214093 214094 214095 214096 214097 214098 240360 240361 240362 240363 240364 240365 240366 240367 240368 240369 240370 240371 240372 240373 240374 268200 268201 268202 268203 268204 270420 270421 270422 270423 277440 277441 277442 277443 277444 277445 277446 277447 298800 298801 298802 298803 298804 298805 298806 298807 298808 298809 298810 298811 298812 298813 298814 298815 298816 298817 298818 298819 298820 359760 359761 359762 378660 378661 378662 378663 378664 378665 385200 385201 385202 385203 385204 385205 385206 385207 385208 385209 385210 385211 385212 387240 387241 387242 387243 387244 387245 387246 387247 387248 387249 387250 387251 387252 387253 387254 387255 387256 387257 387258 387259 387260 407220 407221 407222 407223 407224 407225 407226 407227 407228 407229 420360 420361 420362 420363 420364 420365 420366 420367 420368 420369 420370 420371 420372 420373 420374 420375 420376 420377 420378 420379 420380 420381 495240 495241 495242 495243 495244 495245 495246 495247 495248 495249 495250 495251 495252 495253 495254 538560 538561 538562 538563 538564 538565 538566 538567 538568 538569 538570 538571 538572 538573 538574 538575 538576 538577 538578 538579 538580 539280 539281 539282 539283 539284 539285 539286 539287 539288 539289 539290 539291 539292 539293 539294 539295 539296 539297 539298 539299 539300 544860 544861 544862 544863 544864 544865 544866 544867 544868 544869 544870 544871 544872 544873 544874 544875 544876 544877 544878 544879 549900 549901 549902 549903 549904 549905 602040 602041 602042 602043 602044 602045 602046 602047 602048 602049 602050 602051 602052 602053 602054 625620 625621 625622 625623 625624 625625 625626 625627 625628 628500 628501 628502 628503 628504 651120 651121 651122 651123 651124 651125 651126 667440 667441 667442 667443] INFO 2025-06-26 16:26:10,325 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 16:26:21,305 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.280.01 ERROR 2025-06-26 16:26:21,305 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.280.01 INFO 2025-06-26 16:26:21,354 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_cal.nc INFO 2025-06-26 16:26:26,678 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, 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 16:26:26,685 process.py align():251 [1] Alignment steps for 2010.280.01 INFO 2025-06-26 16:26:26,720 align.py process_cal():139 [1] Processing dorado_2010.280.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.280.01 INFO 2025-06-26 16:26:26,741 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:26:26,744 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:26:26,788 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:26:26,792 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:26:26,837 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:26:26,841 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:26:26,867 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:26:26,867 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:26:26,885 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:26:26,888 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:26:26,931 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:26,935 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:26:26,973 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:26,977 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:26:27,017 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,021 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:26:27,060 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,064 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,105 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,109 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,148 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,151 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,191 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,194 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,232 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,236 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,278 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,281 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,321 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,325 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,366 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,369 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,408 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,412 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,452 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,456 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,495 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,499 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,541 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,545 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,585 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,588 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,631 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,636 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,675 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,679 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,720 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,723 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,762 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,766 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,807 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,811 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,850 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:26:27,853 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:26:27,903 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:26:27,943 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:26:27,981 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:26:28,020 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:26:28,062 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:26:28,116 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.92 INFO 2025-06-26 16:26:28,430 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:26:28,463 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_align.nc INFO 2025-06-26 16:26:28,575 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, 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 16:26:28,578 process.py resample():273 [1] Resampling steps for 2010.280.01 INFO 2025-06-26 16:26:28,579 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:26:28,611 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_align.nc mission netCDF file INFO 2025-06-26 16:26:28,617 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_align.nc mission netCDF file INFO 2025-06-26 16:26:28,619 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-07T18:36:43.023843328 to 2010-10-07T21:54:35.220542208 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:26:28,622 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-07T18:36:01.036719616 to 2010-10-07T21:54:35.220542208 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:26:28,624 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-07T18:36:53.373134336 to 2010-10-07T21:54:35.100550400 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 16:26:28,627 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-07T18:36:21.075346944 to 2010-10-07T21:54:35.060552960 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 16:26:28,628 resample.py get_mission_start_end():1145 [1] isus : 2010-10-07T18:36:53.453128704 to 2010-10-07T21:54:34.480592640 (0 days 00:00:00.739949568 before mission_end) INFO 2025-06-26 16:26:28,630 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-07T18:35:52.277285376 to 2010-10-07T21:54:34.050588160 (0 days 00:00:01.169954048 before mission_end) INFO 2025-06-26 16:26:28,631 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-07T18:35:55.127124480 to 2010-10-07T21:54:35.070552320 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 16:26:28,632 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_align.nc mission netCDF file INFO 2025-06-26 16:26:28,633 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,777 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,804 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,831 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,857 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,882 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,905 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,927 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,949 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,970 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:28,990 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,012 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,033 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,054 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,075 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,096 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,117 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,137 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,159 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,183 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,205 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,228 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,250 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,273 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,295 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,309 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,321 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,332 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,343 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,354 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:29,358 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:26:29,358 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:26:29,814 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:26:29,898 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:26:29,943 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:26:29,964 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:26:29,981 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:26:29,981 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:26:30,012 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:26:30,194 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_1S.nc INFO 2025-06-26 16:26:32,472 create_products.py gulper_odv():401 [1] No gulper times found for 2010.280.01 INFO 2025-06-26 16:26:32,472 process.py archive():337 [1] Archiving steps for 2010.280.01 INFO 2025-06-26 16:26:32,472 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01, BASE_PATH = /data/auv_data INFO 2025-06-26 16:26:32,473 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:26:32,475 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.280.01_1S.nc INFO 2025-06-26 16:26:32,492 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:26:32,493 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.280.01_cal.nc INFO 2025-06-26 16:26:32,578 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:26:32,579 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.280.01_align.nc INFO 2025-06-26 16:26:32,690 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:26:32,709 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,726 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,731 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,746 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,784 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,790 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,809 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,824 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,859 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,865 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010280/2010.280.01 done. INFO 2025-06-26 16:26:32,865 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:26:32,865 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.280.01/dorado_2010.280.01_processing.log /Volumes/AUVCTD/surveys/2010/netcdf