INFO 2025-06-26 14:38:39,127 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 14:38:39,127 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Ryan along north coast across bay overnight - ctdToUse = ctd1 INFO 2025-06-26 14:38:39,127 process.py process_mission():449 [1] Processing AUVCTD mission 2009.085.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:38:39,127 process.py download_process():165 [1] Download and processing steps for 2009.085.02 INFO 2025-06-26 14:38:39,127 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009085/2009.085.02 INFO 2025-06-26 14:38:39,127 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009085/2009.085.02 to /data/auv_data/dorado/missionlogs/2009.085.02 INFO 2025-06-26 14:38:42,381 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.085.02 INFO 2025-06-26 14:38:42,382 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/ctdDriver.log (3749636 bytes) INFO 2025-06-26 14:38:42,653 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.085.02/ctdDriver.log: [ 1460 3212 4707 5255 7751 12122 13064 14147 14210 16996 17497 18382 19738 22018 22668 23951 27662 42316] INFO 2025-06-26 14:38:42,663 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/ctdDriver2.log (3749717 bytes) INFO 2025-06-26 14:38:42,934 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.085.02/ctdDriver2.log: [ 33 230 3504 3771 4430 5301 7077 7202 10637 12229 21648 22501 24213 34758 39282] INFO 2025-06-26 14:38:42,947 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/gps.log (40388 bytes) INFO 2025-06-26 14:38:42,959 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/hydroscatlog.log (3584218 bytes) INFO 2025-06-26 14:38:43,322 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.085.02/hydroscatlog.log: [ 1 209 343 906 3554 4849 6237 16588 19693 21353 21658 35643] INFO 2025-06-26 14:38:43,332 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/navigation.log (12556034 bytes) INFO 2025-06-26 14:38:44,221 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/isuslog.log (249173 bytes) INFO 2025-06-26 14:38:44,249 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.085.02/isuslog.log: [1 2 3 4 5 6 7 8] INFO 2025-06-26 14:38:44,250 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/parosci.log (4343606 bytes) INFO 2025-06-26 14:38:44,617 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/tailCone.log (522187 bytes) INFO 2025-06-26 14:38:44,690 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/biolume.log (2907820 bytes) INFO 2025-06-26 14:38:44,963 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:38:45,124 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.74 seconds INFO 2025-06-26 14:38:45,124 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.085.02/lopc.bin (33722713 bytes) INFO 2025-06-26 14:38:45,124 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:38:45 2025 INFO 2025-06-26 14:38:45,124 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.085.02/parosci.nc INFO 2025-06-26 14:38:45,124 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:38:45,124 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.085.02/parosci.nc INFO 2025-06-26 14:38:45,128 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1238094457.2, sensor_off_time = 1238105134.4 INFO 2025-06-26 14:38:45,128 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10677 seconds. Expecting to read 21354 L frames from the lopc.bin file. INFO 2025-06-26 14:38:45,128 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21354 records from the lopc.bin file. INFO 2025-06-26 14:38:45,255 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-03-26 19:07:37 Z and endTime = 2009-03-26 22:05:34 Z with 21354 records expected to be read from lopc.bin INFO 2025-06-26 14:38:45,255 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.085.02/lopc.bin INFO 2025-06-26 14:38:45,255 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.085.02/lopc.nc INFO 2025-06-26 14:38:45,257 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.085.02/lopc.nc INFO 2025-06-26 14:38:45,257 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.085.02 INFO 2025-06-26 14:38:45,257 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:38:45,418 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:38:45,419 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:38:45,419 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 14:38:45,765 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 14:38:45,766 process.py calibrate():227 [1] Calibration steps for 2009.085.02 INFO 2025-06-26 14:38:45,896 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 14:38:45,898 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:38:46,782 calibrate.py _nudge_pos():1806 [1] 121: 0.090 0.0000140 -0.0000208 1614 5.40 0.384 -0.715 2009-03-26T19:14:59.249744128 INFO 2025-06-26 14:38:46,830 calibrate.py _nudge_pos():1806 [1] 126: 0.080 -0.0000005 -0.0000025 15 0.05 -1.515 -9.777 2009-03-26T19:15:06.249264640 INFO 2025-06-26 14:38:46,987 calibrate.py _nudge_pos():1806 [1] 143: 0.090 0.0000197 -0.0000036 15 0.05 62.770 -14.253 2009-03-26T19:15:25.247963136 INFO 2025-06-26 14:38:47,444 calibrate.py _nudge_pos():1806 [1] 192: 0.080 0.0010077 -0.0010028 8557 28.56 5.232 -6.506 2009-03-26T19:44:47.257257216 INFO 2025-06-26 14:38:48,103 calibrate.py _nudge_pos():1806 [1] 260: 0.090 0.0020523 -0.0007000 7701 25.68 11.854 -5.051 2009-03-26T20:11:35.257101824 INFO 2025-06-26 14:38:48,741 calibrate.py _nudge_pos():1806 [1] 329: 0.090 0.0000112 -0.0000154 15 0.05 35.664 -61.157 2009-03-26T20:12:46.252238336 INFO 2025-06-26 14:38:48,789 calibrate.py _nudge_pos():1806 [1] 334: 0.090 0.0009498 -0.0011475 9251 30.85 4.566 -6.893 2009-03-26T20:43:41.255162112 INFO 2025-06-26 14:38:49,366 calibrate.py _nudge_pos():1806 [1] 396: 0.100 0.0000252 -0.0000126 15 0.05 80.226 -50.227 2009-03-26T20:44:46.250709248 INFO 2025-06-26 14:38:49,385 calibrate.py _nudge_pos():1806 [1] 398: 0.090 0.0019184 -0.0006520 7527 25.10 11.338 -4.814 2009-03-26T21:09:53.257472256 INFO 2025-06-26 14:38:50,131 calibrate.py _nudge_pos():1806 [1] 469: 0.100 0.0007440 -0.0011582 8648 28.83 3.827 -7.444 2009-03-26T21:39:53.254164224 INFO 2025-06-26 14:38:50,818 calibrate.py _nudge_pos():1806 [1] 534: 0.100 0.0020120 -0.0005116 7315 24.38 12.241 -3.888 2009-03-26T22:05:20.249557760 INFO 2025-06-26 14:38:50,967 calibrate.py _nudge_pos():1862 [1] 516: - - - 1 0.00 - - INFO 2025-06-26 14:38:50,967 calibrate.py _nudge_pos():1868 [1] Points in final series = 53195 INFO 2025-06-26 14:38:51,040 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=60) for self.args.mission=2009.085.02 INFO 2025-06-26 14:38:51,043 calibrate.py _depth_process():2175 [1] Setting 129 depths values to NaN WARNING 2025-06-26 14:38:51,045 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:38:56,913 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:38:59,959 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:39:00,313 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:39:00,315 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.085.02/ctd1.nc INFO 2025-06-26 14:39:00,316 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:39:00,317 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 14:39:00,317 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:39:02,645 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:39:02,963 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:39:02,965 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.085.02/ctd2.nc INFO 2025-06-26 14:39:02,966 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 14:39:02,967 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 14:39:02,967 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:39:03,347 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:39:03,881 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 77 120 121 122 123 124 125 126 127 128 240 241 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 2040 2041 2042 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 4320 4321 4322 4323 4324 4325 4326 8340 8341 8342 10980 10981 10982 10983 10984 10985 10986 10987 10988 12000 12001 12002 12003 12004 12005 12006 12007 12008 12960 12961 12962 12963 12964 12965 12966 12967 12968 12969 12970 12971 12972 12973 16440 16441 16442 24480 24481 24482 24483 24484 24485 24486 24487 24488 24489 24490 24491 24492 24493 24494 28980 28981 28982 28983 28984 28985 28986 28987 28988 28989 31440 31441 31442 31443 45360 45361 45362 45363 45364 45365 45366 45367 45368 45369 45370 45371 51960 51961 51962 51963 51964 51965 51966 52680 52681 52682 52683 52684 52685 52686 52687 52688 52689 52690 52691 52692 54000 54001 54002 54003 54004 54005 54006 54007 54008 54009 54010 54011 54300 54301 60780 60781 60782 60783 60784 71100 71101 71102 71103 71104 71105 71106 71107 71108 71109 71110 71111 71112 71113 71114 71115 71116 72360 72361 72362 72363 72364 72365 72366 73860 73861 73862 73863 73864 73865 73866 73867 73868 73869 76920 76921 76922 76923 76924 76925 76926 76927 76928 80580 80581 80582 80583 80584 80585 80586 90180 90181 90182 90183 90184 90185 100740 100741 100742 100743 100744 100745 100746 100747 100748 100749 101340 101341 101342 101343 101344 101345 101346 101347 101348 101349 101350 101351 101352 101353 118020 118021 118022 118023 118024 118025 118026 118027 118028 118029 118030 118031 122100 122101 122102 122103 122104 122105 122106 151200 151201 151202 151203 151204 151205 151206 170700 170701 170702 170703 170704 170705 170706 170707 170708 176460 176461 176462 176463 176464 176465 183600 208620 208621 208622 208623 208624 208625 208626 208627 208628 208629 208630 208631 208632 208633 208634 208635 214920 214921 214922 214923 214924 214925 225360 225361 225362 226380 226381 226382 226383 226384 226385 226386 226387 226388 267000 267001 267002 267003 267004 267005 267006 267007 267008 267009 267010 267011 277500 277501 277502 277503 277504 277505 277506 277507 277508 296160 296161 296162 296163 296164 296165 296166 296167 296168 296169 296170 296171 296172 296173 296174 296175 296176 297840 297841 297842 297843 297844 297845 297846 297847 297848 297849 325860 325861 325862 325863 325864 325865 325866 325867 325868 325869 325870 325871 325872 325873 325874 325875 332040 332041 332042 332043 332044 332045 332046 332047 332048 332049 332050 332051 332052 332053 390540 390541 390542 390543 390544 392460 392461 392462 392463 392464 392465 392466 392467 392468 409680 409681 409682 409683 409684 409685 409686 409687 409688 409689 438720 438721 438722 438723 438724 438725 438726 438727 438728 438729 438730 438731 438732 448980 448981 448982 448983 448984 448985 457140 457141 457142 457143 457144 457145 457146 457147 457148 457149 457150 457151 457152 457153 457154 457155 465660 465661 465662 465663 465664 465665 465666 465667 465668 465669 465670 465671 465672 465673 465674 483120 483121 483122 483123 483124 483125 483126 483127 483128 483129 483130 483131 523140 523141 523142 523143 523144 523145 523146 523147 523148 523149 550260 550261 550262 571920 571921 571922 571923 571924 571925 571926 582240 582241 582242 582243 582244 582245 582246 582247 582248 582249 582250 582251 621480 626880 626881 636540 636541 636542 636543 636544 636545 636546 636547 636548 636549] INFO 2025-06-26 14:39:03,979 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:39:03,985 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 14:39:03,985 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2009.085.02 ERROR 2025-06-26 14:39:03,985 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.085.02 INFO 2025-06-26 14:39:03,997 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_cal.nc INFO 2025-06-26 14:39:07,345 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_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 14:39:07,350 process.py align():251 [1] Alignment steps for 2009.085.02 INFO 2025-06-26 14:39:07,376 align.py process_cal():139 [1] Processing dorado_2009.085.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.085.02 INFO 2025-06-26 14:39:07,394 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:39:07,397 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:39:07,437 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:39:07,441 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:39:07,482 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:39:07,485 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:39:07,509 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:39:07,510 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:39:07,525 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:39:07,528 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:39:07,568 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,571 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,607 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,610 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,647 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,650 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,685 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,688 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,724 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,727 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,762 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,765 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,801 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,805 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,842 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,845 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,882 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,886 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,921 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,925 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:07,964 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:07,967 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,003 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,006 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,043 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,046 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,082 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,085 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,123 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,127 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,162 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,166 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,203 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,206 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,242 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,246 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,283 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,286 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,321 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.085.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:39:08,324 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:39:08,368 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:39:08,400 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:39:08,432 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:39:08,466 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:39:08,499 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 14:39:08,514 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_align.nc INFO 2025-06-26 14:39:08,574 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_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 14:39:08,577 process.py resample():273 [1] Resampling steps for 2009.085.02 INFO 2025-06-26 14:39:08,578 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:39:08,600 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_align.nc mission netCDF file INFO 2025-06-26 14:39:08,605 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_align.nc mission netCDF file INFO 2025-06-26 14:39:08,607 resample.py get_mission_start_end():1145 [1] navigation: 2009-03-26T19:08:09.137838848 to 2009-03-26T22:05:34.448584960 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:39:08,608 resample.py get_mission_start_end():1145 [1] hs2 : 2009-03-26T19:07:46.439393792 to 2009-03-26T22:05:34.308594688 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 14:39:08,610 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-03-26T19:08:04.228175104 to 2009-03-26T22:05:34.368590592 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 14:39:08,612 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-03-26T19:08:04.228175104 to 2009-03-26T22:05:34.308594688 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 14:39:08,613 resample.py get_mission_start_end():1145 [1] isus : 2009-03-26T19:08:36.595957760 to 2009-03-26T22:05:33.388657920 (0 days 00:00:01.059927040 before mission_end) INFO 2025-06-26 14:39:08,615 resample.py get_mission_start_end():1145 [1] biolume : 2009-03-26T19:07:36.040071936 to 2009-03-26T22:05:33.468617984 (0 days 00:00:00.979966976 before mission_end) INFO 2025-06-26 14:39:08,616 resample.py get_mission_start_end():1145 [1] tailcone : 2009-03-26T19:07:41.589725952 to 2009-03-26T22:05:33.648640000 (0 days 00:00:00.799944960 before mission_end) INFO 2025-06-26 14:39:08,617 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_align.nc mission netCDF file INFO 2025-06-26 14:39:08,617 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,748 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,772 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,796 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,820 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,843 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,865 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,886 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,906 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,926 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,945 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,964 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:08,984 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,003 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,022 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,041 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,060 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,082 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,102 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,122 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,142 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,162 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,182 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,195 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,206 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,217 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,229 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,242 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:39:09,392 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_1S.nc INFO 2025-06-26 14:39:11,237 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 14:39:17,804 create_products.py gulper_odv():522 [1] Wrote 6 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.085.02/dorado_2009.085.02_1S_Gulper.txt INFO 2025-06-26 14:39:17,804 process.py archive():337 [1] Archiving steps for 2009.085.02 INFO 2025-06-26 14:39:17,805 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02, BASE_PATH = /data/auv_data INFO 2025-06-26 14:39:17,805 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 14:39:17,806 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.085.02_1S.nc INFO 2025-06-26 14:39:17,819 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:39:17,820 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.085.02_cal.nc INFO 2025-06-26 14:39:17,871 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:39:17,872 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.085.02_align.nc INFO 2025-06-26 14:39:17,913 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:39:17,929 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:17,945 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:17,949 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:17,963 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:17,997 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:18,003 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:18,019 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:18,026 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:18,057 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:18,063 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009085/2009.085.02 done. INFO 2025-06-26 14:39:18,063 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:39:18,064 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.085.02_1S_Gulper.txt INFO 2025-06-26 14:39:18,069 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.085.02/dorado_2009.085.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 14:39:18,069 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.085.02/dorado_2009.085.02_processing.log /Volumes/AUVCTD/surveys/2009/netcdf