Execution of AUVprocess_main version 1.87 at 2019-02-21T16:54:15Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2018, ['156.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2018.156.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/navigation.nc') Creating vector time with 446721 elements. Creating vector mPos_x with 446721 elements. Creating vector time with 446721 elements. Creating vector mPos_y with 446721 elements. Creating vector time with 446721 elements. Creating vector mDepth with 446721 elements. Creating vector time with 446721 elements. Creating vector mGpsNorth with 446721 elements. Creating vector time with 446721 elements. Creating vector mGpsEast with 446721 elements. Creating vector time with 446721 elements. Creating vector mGpsValid with 446721 elements. Creating vector time with 446721 elements. Creating vector mPhi with 446721 elements. Creating vector time with 446721 elements. Creating vector mTheta with 446721 elements. Creating vector time with 446721 elements. Creating vector mPsi with 446721 elements. Creating vector time with 446721 elements. Creating vector mOmega_x with 446721 elements. Creating vector time with 446721 elements. Creating vector mOmega_y with 446721 elements. Creating vector time with 446721 elements. Creating vector mOmega_z with 446721 elements. Creating vector time with 446721 elements. Creating vector mPsaRange with 446721 elements. Creating vector time with 446721 elements. Creating vector mAltitude with 446721 elements. Creating vector time with 446721 elements. Creating vector multibeamAltitude with 446721 elements. Creating vector time with 446721 elements. Creating vector mDvlAltitude with 446721 elements. Creating vector time with 446721 elements. Creating vector mEchoAltitude with 446721 elements. Creating vector time with 446721 elements. Creating vector mEchoHorizRange with 446721 elements. Creating vector time with 446721 elements. Creating vector mEchoAltitudeLast with 446721 elements. Creating vector time with 446721 elements. Creating vector mEchoHorizRangeLast with 446721 elements. Creating vector time with 446721 elements. Creating vector mEchoNumOfPings with 446721 elements. Creating vector time with 446721 elements. Creating vector nadirCnts with 446721 elements. Creating vector time with 446721 elements. Creating vector obstacleCnts with 446721 elements. Creating vector time with 446721 elements. Creating vector nGoodNadirBeams with 446721 elements. Creating vector time with 446721 elements. Creating vector medianNadirBeamNo with 446721 elements. Creating vector time with 446721 elements. Creating vector mWaterSpeed with 446721 elements. Creating vector time with 446721 elements. Creating vector mDvlValid with 446721 elements. Creating vector time with 446721 elements. Creating vector mDvlNewData with 446721 elements. Creating vector time with 446721 elements. Creating vector mDeltaT with 446721 elements. Creating vector time with 446721 elements. Creating vector nfix with 446721 elements. Creating vector time with 446721 elements. Creating vector efix with 446721 elements. Creating vector time with 446721 elements. Creating vector filter_north with 446721 elements. Creating vector time with 446721 elements. Creating vector filter_east with 446721 elements. Creating vector time with 446721 elements. Creating vector filter_depth with 446721 elements. Creating vector time with 446721 elements. Creating vector north_current with 446721 elements. Creating vector time with 446721 elements. Creating vector east_current with 446721 elements. Creating vector time with 446721 elements. Creating vector speed_bias with 446721 elements. Creating vector time with 446721 elements. Creating vector heading_bias with 446721 elements. Creating vector time with 446721 elements. Creating vector latitude with 446721 elements. Creating vector time with 446721 elements. Creating vector longitude with 446721 elements. Creating vector time with 446721 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/navigation.nc'); processNav(): median of positive valued depths = 31.273 processNav(): Finding depths less than 218.9112 and times > 0 processNav(): length(Nav.depth) = 446721 processNav(): length(gindx) = 446721 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/gps.nc') Creating vector time with 10113 elements. Creating vector hours with 10113 elements. Creating vector time with 10113 elements. Creating vector minutes with 10113 elements. Creating vector time with 10113 elements. Creating vector seconds with 10113 elements. Creating vector time with 10113 elements. Creating vector centiSeconds with 10113 elements. Creating vector time with 10113 elements. Creating vector latitude with 10113 elements. Creating vector time with 10113 elements. Creating vector longitude with 10113 elements. Creating vector time with 10113 elements. Creating vector quality with 10113 elements. Creating vector time with 10113 elements. Creating vector numberOfSatellites with 10113 elements. Creating vector time with 10113 elements. Creating vector hdop with 10113 elements. Creating vector time with 10113 elements. Creating vector antennaHeight with 10113 elements. Creating vector time with 10113 elements. Creating vector geoHeight with 10113 elements. Creating vector time with 10113 elements. Creating vector dgpsDataAge with 10113 elements. Creating vector time with 10113 elements. Creating vector dgpsRSID with 10113 elements. Creating vector time with 10113 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/parosci.nc') Creating vector time with 889587 elements. Creating vector depth with 889587 elements. Creating vector time with 889587 elements. Creating vector temp with 889587 elements. Creating vector time with 889587 elements. Creating vector pressure with 889587 elements. Creating vector time with 889587 elements. Creating vector temp_period with 889587 elements. Creating vector time with 889587 elements. Creating vector pres_period with 889587 elements. Creating vector time with 889587 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.59053 max(Depth.data) = 103.8853 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.59053 max(Depth.data) = 103.8853 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/hydroscatlog.nc') Creating vector time with 357327 elements. Creating vector Seconds with 357327 elements. Creating vector time with 357327 elements. Creating vector HundrethsOfSeconds with 357327 elements. Creating vector time with 357327 elements. Creating vector Snorm1 with 357327 elements. Creating vector time with 357327 elements. Creating vector Snorm2 with 357327 elements. Creating vector time with 357327 elements. Creating vector Snorm3 with 357327 elements. Creating vector time with 357327 elements. Creating vector Gain_Status_1 with 357327 elements. Creating vector time with 357327 elements. Creating vector Gain_Status_2 with 357327 elements. Creating vector time with 357327 elements. Creating vector Gain_Status_3 with 357327 elements. Creating vector time with 357327 elements. Creating vector RawDepthValue with 357327 elements. Creating vector time with 357327 elements. Creating vector RawTempValue with 357327 elements. Creating vector time with 357327 elements. Creating vector Temperature with 357327 elements. Creating vector time with 357327 elements. Creating vector ErrorValue with 357327 elements. Creating vector time with 357327 elements. Creating vector bb470 with 357327 elements. Creating vector time with 357327 elements. Creating vector bb676 with 357327 elements. Creating vector time with 357327 elements. Creating vector fl676u with 357327 elements. Creating vector time with 357327 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ctdDriver.nc') Creating vector time with 357350 elements. Creating vector conductivity with 357350 elements. Creating vector time with 357350 elements. Creating vector temperature with 357350 elements. Creating vector time with 357350 elements. Creating vector cond_frequency with 357350 elements. Creating vector time with 357350 elements. Creating vector temp_frequency with 357350 elements. Creating vector time with 357350 elements. Creating vector spare with 357350 elements. Creating vector time with 357350 elements. Creating vector humidity with 357350 elements. Creating vector time with 357350 elements. Creating vector flow1 with 357350 elements. Creating vector time with 357350 elements. Creating vector CDOM with 357350 elements. Creating vector time with 357350 elements. Creating vector dissolvedO2 with 357350 elements. Creating vector time with 357350 elements. Creating vector salinity with 357350 elements. Creating vector time with 357350 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ctdDriver2.nc') Creating vector time with 357417 elements. Creating vector conductivity with 357417 elements. Creating vector time with 357417 elements. Creating vector temperature with 357417 elements. Creating vector time with 357417 elements. Creating vector cond_frequency with 357417 elements. Creating vector time with 357417 elements. Creating vector temp_frequency with 357417 elements. Creating vector time with 357417 elements. Creating vector flow2 with 357417 elements. Creating vector time with 357417 elements. Creating vector spare with 357417 elements. Creating vector time with 357417 elements. Creating vector salinity with 357417 elements. Creating vector time with 357417 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/isuslog.nc') Creating vector time with 69721 elements. Creating vector isusNitrate with 69721 elements. Creating vector time with 69721 elements. Creating vector isusTemp with 69721 elements. Creating vector time with 69721 elements. Creating vector isusQuality with 69721 elements. Creating vector time with 69721 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/biolume.nc') Creating vector time with 87866 elements. Creating vector rrr with 87866 elements. Creating vector time with 87866 elements. Creating vector cal_striing with 87866 elements. Creating vector time with 87866 elements. Creating vector avg_biolume with 87866 elements. Creating vector time with 87866 elements. Creating vector pump with 87866 elements. Creating vector time with 87866 elements. Creating vector system_voltage with 87866 elements. Creating vector time with 87866 elements. Creating vector flow with 87866 elements. Creating vector time with 87866 elements. Creating vector HV with 87866 elements. Creating vector time with 87866 elements. Creating vector reserved with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_0 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_1 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_2 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_3 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_4 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_5 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_6 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_7 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_8 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_9 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_10 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_11 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_12 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_13 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_14 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_15 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_16 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_17 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_18 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_19 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_20 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_21 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_22 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_23 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_24 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_25 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_26 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_27 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_28 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_29 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_30 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_31 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_32 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_33 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_34 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_35 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_36 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_37 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_38 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_39 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_40 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_41 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_42 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_43 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_44 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_45 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_46 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_47 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_48 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_49 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_50 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_51 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_52 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_53 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_54 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_55 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_56 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_57 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_58 with 87866 elements. Creating vector time with 87866 elements. Creating vector raw_59 with 87866 elements. Creating vector time with 87866 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (2096 x 994) with 2083424 elements. Creating vector time with 2096 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (2096 x 994) with 2083424 elements. Creating vector time with 2096 elements. Creating vector bin with 994 elements. Creating matrix countList (2096 x 994) with 2083424 elements. Creating vector time with 2096 elements. Creating vector bin with 994 elements. Creating vector LCcount with 2096 elements. Creating vector time with 2096 elements. Creating vector transCount with 2096 elements. Creating vector time with 2096 elements. Creating vector nonTransCount with 2096 elements. Creating vector time with 2096 elements. Creating vector ai_mean with 2096 elements. Creating vector time with 2096 elements. Creating vector ai_min with 2096 elements. Creating vector time with 2096 elements. Creating vector ai_max with 2096 elements. Creating vector time with 2096 elements. Creating vector ai_std with 2096 elements. Creating vector time with 2096 elements. Creating vector esd_mean with 2096 elements. Creating vector time with 2096 elements. Creating vector esd_min with 2096 elements. Creating vector time with 2096 elements. Creating vector esd_max with 2096 elements. Creating vector time with 2096 elements. Creating vector esd_std with 2096 elements. Creating vector time with 2096 elements. Creating vector countSum with 2096 elements. Creating vector time with 2096 elements. Creating vector snapshot with 2096 elements. Creating vector time with 2096 elements. Creating vector threshold with 2096 elements. Creating vector time with 2096 elements. Creating vector sampleCount with 2096 elements. Creating vector time with 2096 elements. Creating vector flowCount with 2096 elements. Creating vector time with 2096 elements. Creating vector flowTime with 2096 elements. Creating vector time with 2096 elements. Creating vector bufferStatus with 2096 elements. Creating vector time with 2096 elements. Creating vector laserLevel with 2096 elements. Creating vector time with 2096 elements. Creating vector counter with 2096 elements. Creating vector time with 2096 elements. Creating vector counterPeriod with 2096 elements. Creating vector time with 2096 elements. Creating vector laserControl with 2096 elements. Creating vector time with 2096 elements. Creating vector countUnknownFrameCharacter with 2096 elements. Creating vector time with 2096 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 2096 elements. Creating vector time with 2096 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 2096 elements. Creating vector time with 2096 elements. Creating vector flowSpeed with 2096 elements. Creating vector time with 2096 elements. Creating vector countShortLFrameError with 2096 elements. Creating vector time with 2096 elements. Creating vector countGarbledLFrame with 2096 elements. Creating vector time with 2096 elements. Creating vector cFrameEsecs with 2096 elements. Creating vector time with 2096 elements. Creating vector correctedSampleCountList with 2096 elements. Creating vector time with 2096 elements. Creating vector time with 2096 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018.156.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018.156.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 22 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 412 Gridding with nix = 1236, iZ = 205 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 430566 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 430566 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 120672 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 06/05/2018 09:30 to 06/06/2018 12:30 swr = 654.0181 899.4343 978.6525 NaN NaN 945.0867 778.9398 598.0117 413.2875 220.7312 50.3351 6.1138 1.5659 1.3902 1.3780 1.2886 1.5439 1.6659 1.4569 1.4455 5.4004 47.0168 93.1976 64.1287 239.4378 518.9489 977.1460 997.3500 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2018156_GulperTimes.txt && touch ../results/2018156_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018156/2018.156.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2018/2018156/2018.156.00/syslog -startEsecs 1528223402.8842 -surveyName Dorado389_2018_156_00_156_00 >> ../results/2018156_GulperTimes.txt Executing: removeGulpDups.py ../results/2018156_GulperTimes.txt Bottle: 0 Time: 1528228013.73 Depth: 8.1268 Dist: 4.7338 Bottle: 1 Time: 1528230248.14 Depth: 9.4111 Dist: 7.3427 Bottle: 2 Time: 1528233623.93 Depth: 6.5956 Dist: 11.0613 Bottle: 3 Time: 1528242916.53 Depth: 1.8742 Dist: 20.6503 Bottle: 4 Time: 1528244950.93 Depth: 3.5851 Dist: 22.3008 Bottle: 5 Time: 1528249857.73 Depth: 24.6946 Dist: 25.5761 Bottle: 6 Time: 1528265791.53 Depth: 12.4008 Dist: 38.779 Bottle: 7 Time: 1528268442.73 Depth: 11.5511 Dist: 41.5007 Bottle: 8 Time: 1528269517.74 Depth: 18.4719 Dist: 42.699 Bottle: 9 Time: 1528272075.13 Depth: 23.0051 Dist: 45.0436 Bottle: 10 Time: 1528273258.93 Depth: 13.2926 Dist: 46.3117 Bottle: 11 Time: 1528274297.73 Depth: 1.9904 Dist: 47.2012 Bottle: 12 Time: 1528276213.14 Depth: 6.6166 Dist: 49.2648 Bottle: 13 Time: 1528286042.33 Depth: 3.2124 Dist: 58.3359 Bottle: 14 Time: 1528291353.33 Depth: 5.4027 Dist: 60.5002 Bottle: 15 Time: 1528296858.73 Depth: 3.3362 Dist: 64.2613 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_2column.png Elapsed time to save image: 11 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_biolume.png Elapsed time to save image: 39 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_lopc.png Elapsed time to save image: 10 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_2column.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing KML files ... KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2018_156_00_156_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.kml... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2018_156_00_156_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 420) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 14 NaNs found in bbpBlue. Interpolating anyway. 31 NaNs found in bbpRed. Interpolating anyway. 13 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 2522 NaN values in array of lon that is 69720 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 67198 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 67198 are not equal to number of Lat lon points = 69720 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.txt... Copied to /mbari/AUVCTD/surveys/2018/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2018/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 14 NaNs found in bbpBlue. Interpolating anyway. 31 NaNs found in bbpRed. Interpolating anyway. 13 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2018/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.nc... Copied to /mbari/AUVCTD/surveys/2018/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2018/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018_156_00_156_00.mat... Copied to /mbari/AUVCTD/surveys/2018/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2018_156_00_156_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2018_156_00_156_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2018.156.00.mat Processing time: 295 seconds