Execution of AUVprocess_main version 1.88 at 2021-07-29T18:10:31Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2019, ['196.04'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2019.196.04 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/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/2019/2019196/2019.196.04/navigation.nc') Creating vector time with 421943 elements. Creating vector mPos_x with 421943 elements. Creating vector time with 421943 elements. Creating vector mPos_y with 421943 elements. Creating vector time with 421943 elements. Creating vector mDepth with 421943 elements. Creating vector time with 421943 elements. Creating vector mGpsNorth with 421943 elements. Creating vector time with 421943 elements. Creating vector mGpsEast with 421943 elements. Creating vector time with 421943 elements. Creating vector mGpsValid with 421943 elements. Creating vector time with 421943 elements. Creating vector mPhi with 421943 elements. Creating vector time with 421943 elements. Creating vector mTheta with 421943 elements. Creating vector time with 421943 elements. Creating vector mPsi with 421943 elements. Creating vector time with 421943 elements. Creating vector mOmega_x with 421943 elements. Creating vector time with 421943 elements. Creating vector mOmega_y with 421943 elements. Creating vector time with 421943 elements. Creating vector mOmega_z with 421943 elements. Creating vector time with 421943 elements. Creating vector mPsaRange with 421943 elements. Creating vector time with 421943 elements. Creating vector mAltitude with 421943 elements. Creating vector time with 421943 elements. Creating vector multibeamAltitude with 421943 elements. Creating vector time with 421943 elements. Creating vector mDvlAltitude with 421943 elements. Creating vector time with 421943 elements. Creating vector mEchoAltitude with 421943 elements. Creating vector time with 421943 elements. Creating vector mEchoHorizRange with 421943 elements. Creating vector time with 421943 elements. Creating vector mEchoAltitudeLast with 421943 elements. Creating vector time with 421943 elements. Creating vector mEchoHorizRangeLast with 421943 elements. Creating vector time with 421943 elements. Creating vector mEchoNumOfPings with 421943 elements. Creating vector time with 421943 elements. Creating vector nadirCnts with 421943 elements. Creating vector time with 421943 elements. Creating vector obstacleCnts with 421943 elements. Creating vector time with 421943 elements. Creating vector nGoodNadirBeams with 421943 elements. Creating vector time with 421943 elements. Creating vector medianNadirBeamNo with 421943 elements. Creating vector time with 421943 elements. Creating vector mWaterSpeed with 421943 elements. Creating vector time with 421943 elements. Creating vector mDvlValid with 421943 elements. Creating vector time with 421943 elements. Creating vector mDvlNewData with 421943 elements. Creating vector time with 421943 elements. Creating vector mDeltaT with 421943 elements. Creating vector time with 421943 elements. Creating vector nfix with 421943 elements. Creating vector time with 421943 elements. Creating vector efix with 421943 elements. Creating vector time with 421943 elements. Creating vector filter_north with 421943 elements. Creating vector time with 421943 elements. Creating vector filter_east with 421943 elements. Creating vector time with 421943 elements. Creating vector filter_depth with 421943 elements. Creating vector time with 421943 elements. Creating vector north_current with 421943 elements. Creating vector time with 421943 elements. Creating vector east_current with 421943 elements. Creating vector time with 421943 elements. Creating vector speed_bias with 421943 elements. Creating vector time with 421943 elements. Creating vector heading_bias with 421943 elements. Creating vector time with 421943 elements. Creating vector latitude with 421943 elements. Creating vector time with 421943 elements. Creating vector longitude with 421943 elements. Creating vector time with 421943 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/navigation.nc'); processNav(): median of positive valued depths = 31.0042 processNav(): Finding depths less than 217.0297 and times > 0 processNav(): length(Nav.depth) = 421943 processNav(): length(gindx) = 421943 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/2019/2019196/2019.196.04/gps.nc') Creating vector time with 16474 elements. Creating vector hours with 16474 elements. Creating vector time with 16474 elements. Creating vector minutes with 16474 elements. Creating vector time with 16474 elements. Creating vector seconds with 16474 elements. Creating vector time with 16474 elements. Creating vector centiSeconds with 16474 elements. Creating vector time with 16474 elements. Creating vector latitude with 16474 elements. Creating vector time with 16474 elements. Creating vector longitude with 16474 elements. Creating vector time with 16474 elements. Creating vector quality with 16474 elements. Creating vector time with 16474 elements. Creating vector numberOfSatellites with 16474 elements. Creating vector time with 16474 elements. Creating vector hdop with 16474 elements. Creating vector time with 16474 elements. Creating vector antennaHeight with 16474 elements. Creating vector time with 16474 elements. Creating vector geoHeight with 16474 elements. Creating vector time with 16474 elements. Creating vector dgpsDataAge with 16474 elements. Creating vector time with 16474 elements. Creating vector dgpsRSID with 16474 elements. Creating vector time with 16474 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/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/2019/2019196/2019.196.04/parosci.nc') Creating vector time with 840226 elements. Creating vector depth with 840226 elements. Creating vector time with 840226 elements. Creating vector temp with 840226 elements. Creating vector time with 840226 elements. Creating vector pressure with 840226 elements. Creating vector time with 840226 elements. Creating vector temp_period with 840226 elements. Creating vector time with 840226 elements. Creating vector pres_period with 840226 elements. Creating vector time with 840226 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.49142 max(Depth.data) = 203.211 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.49142 max(Depth.data) = 203.211 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/2019/2019196/2019.196.04/hydroscatlog.nc') Creating vector time with 337446 elements. Creating vector Seconds with 337446 elements. Creating vector time with 337446 elements. Creating vector HundrethsOfSeconds with 337446 elements. Creating vector time with 337446 elements. Creating vector Snorm1 with 337446 elements. Creating vector time with 337446 elements. Creating vector Snorm2 with 337446 elements. Creating vector time with 337446 elements. Creating vector Snorm3 with 337446 elements. Creating vector time with 337446 elements. Creating vector Gain_Status_1 with 337446 elements. Creating vector time with 337446 elements. Creating vector Gain_Status_2 with 337446 elements. Creating vector time with 337446 elements. Creating vector Gain_Status_3 with 337446 elements. Creating vector time with 337446 elements. Creating vector RawDepthValue with 337446 elements. Creating vector time with 337446 elements. Creating vector RawTempValue with 337446 elements. Creating vector time with 337446 elements. Creating vector Temperature with 337446 elements. Creating vector time with 337446 elements. Creating vector ErrorValue with 337446 elements. Creating vector time with 337446 elements. Creating vector bb470 with 337446 elements. Creating vector time with 337446 elements. Creating vector bb676 with 337446 elements. Creating vector time with 337446 elements. Creating vector fl676u with 337446 elements. Creating vector time with 337446 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/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/2019/2019196/2019.196.04/ctdDriver.nc') Creating vector time with 337524 elements. Creating vector conductivity with 337524 elements. Creating vector time with 337524 elements. Creating vector temperature with 337524 elements. Creating vector time with 337524 elements. Creating vector cond_frequency with 337524 elements. Creating vector time with 337524 elements. Creating vector temp_frequency with 337524 elements. Creating vector time with 337524 elements. Creating vector spare with 337524 elements. Creating vector time with 337524 elements. Creating vector humidity with 337524 elements. Creating vector time with 337524 elements. Creating vector flow1 with 337524 elements. Creating vector time with 337524 elements. Creating vector CDOM with 337524 elements. Creating vector time with 337524 elements. Creating vector dissolvedO2 with 337524 elements. Creating vector time with 337524 elements. Creating vector salinity with 337524 elements. Creating vector time with 337524 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/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/2019/2019196/2019.196.04/ctdDriver2.nc') Creating vector time with 337525 elements. Creating vector conductivity with 337525 elements. Creating vector time with 337525 elements. Creating vector temperature with 337525 elements. Creating vector time with 337525 elements. Creating vector cond_frequency with 337525 elements. Creating vector time with 337525 elements. Creating vector temp_frequency with 337525 elements. Creating vector time with 337525 elements. Creating vector flow2 with 337525 elements. Creating vector time with 337525 elements. Creating vector spare with 337525 elements. Creating vector time with 337525 elements. Creating vector salinity with 337525 elements. Creating vector time with 337525 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/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/2019/2019196/2019.196.04/isuslog.nc') Creating vector time with 65909 elements. Creating vector isusNitrate with 65909 elements. Creating vector time with 65909 elements. Creating vector isusTemp with 65909 elements. Creating vector time with 65909 elements. Creating vector isusQuality with 65909 elements. Creating vector time with 65909 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/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 71) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 227)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 71) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 227)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/biolume.nc') Creating vector time with 82996 elements. Creating vector rrr with 82996 elements. Creating vector time with 82996 elements. Creating vector cal_striing with 82996 elements. Creating vector time with 82996 elements. Creating vector avg_biolume with 82996 elements. Creating vector time with 82996 elements. Creating vector pump with 82996 elements. Creating vector time with 82996 elements. Creating vector system_voltage with 82996 elements. Creating vector time with 82996 elements. Creating vector flow with 82996 elements. Creating vector time with 82996 elements. Creating vector HV with 82996 elements. Creating vector time with 82996 elements. Creating vector reserved with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_0 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_1 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_2 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_3 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_4 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_5 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_6 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_7 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_8 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_9 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_10 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_11 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_12 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_13 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_14 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_15 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_16 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_17 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_18 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_19 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_20 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_21 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_22 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_23 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_24 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_25 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_26 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_27 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_28 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_29 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_30 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_31 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_32 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_33 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_34 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_35 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_36 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_37 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_38 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_39 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_40 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_41 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_42 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_43 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_44 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_45 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_46 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_47 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_48 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_49 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_50 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_51 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_52 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_53 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_54 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_55 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_56 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_57 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_58 with 82996 elements. Creating vector time with 82996 elements. Creating vector raw_59 with 82996 elements. Creating vector time with 82996 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/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/2019/2019196/2019.196.04/lopc.nc') Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/lopc.nc.dods?. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/lopc.nc'); Error: Error while reading the URL: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019196/2019.196.04/lopc.nc.das. The OPeNDAP server returned the following message: Not Found: The data source or server could not be found. Often this means that the OPeNDAP server is missing or needs attention; Please contact the server administrator. *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019.196.04.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.cvs/src/matlab/doradosdp/results/Dorado389_2019.196.04.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 31 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.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 = 460 Gridding with nix = 1380, iZ = 404 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 Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. 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 No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 396740 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 396740 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 145548 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 07/15/2019 10:29 to 07/16/2019 11:30 swr = 825.7241 947.2726 993.4000 992.0129 927.2851 786.0215 581.8173 392.7554 189.6063 55.4078 7.4516 1.7333 1.7747 1.6014 1.6413 1.6587 1.5080 1.4587 1.5080 1.8239 20.4688 67.9201 156.7213 251.5838 400.4705 617.8568 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2019196_GulperTimes.txt && touch ../results/2019196_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/2019/2019196/2019.196.04/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2019/2019196/2019.196.04/syslog -startEsecs 1563218704.4726 -surveyName Dorado389_2019_196_04_196_04 >> ../results/2019196_GulperTimes.txt Executing: removeGulpDups.py ../results/2019196_GulperTimes.txt Bottle: 0 Time: 1563220429.0745 Depth: 200.0123 Dist: 1.8087 Bottle: 1 Time: 1563220553.2659 Depth: 149.9675 Dist: 1.9573 Bottle: 2 Time: 1563220663.6684 Depth: 99.9153 Dist: 2.0989 Bottle: 3 Time: 1563220713.065 Depth: 79.9703 Dist: 2.1492 Bottle: 4 Time: 1563220766.2714 Depth: 59.9189 Dist: 2.2148 Bottle: 5 Time: 1563220818.6678 Depth: 39.9774 Dist: 2.2846 Bottle: 6 Time: 1563220850.0656 Depth: 29.9592 Dist: 2.3245 Bottle: 7 Time: 1563220882.6734 Depth: 19.941 Dist: 2.3667 Bottle: 8 Time: 1563220916.2711 Depth: 9.9191 Dist: 2.4109 Bottle: 9 Time: 1563220967.4676 Depth: -0.143 Dist: 2.4625 Bottle: 10 Time: 1563251482.5725 Depth: 200.0547 Dist: 36.1239 Bottle: 11 Time: 1563251600.9744 Depth: 149.98 Dist: 36.2635 Bottle: 12 Time: 1563251707.9771 Depth: 99.9205 Dist: 36.3822 Bottle: 13 Time: 1563251759.3735 Depth: 79.9046 Dist: 36.4462 Bottle: 14 Time: 1563251810.78 Depth: 59.9323 Dist: 36.5119 Bottle: 15 Time: 1563251860.9766 Depth: 39.8948 Dist: 36.577 Bottle: 16 Time: 1563251888.3747 Depth: 29.9659 Dist: 36.6065 Bottle: 17 Time: 1563251917.3727 Depth: 19.9614 Dist: 36.6351 Bottle: 18 Time: 1563251946.1707 Depth: 9.905 Dist: 36.6621 Bottle: 19 Time: 1563251978.5785 Depth: -0.22954 Dist: 36.6966 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_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.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_2column.png Elapsed time to save image: 20 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.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_biolume.png Elapsed time to save image: 59 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.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_lopc.png Elapsed time to save image: 14 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_2column.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_biolume.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_lopc.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 2 NaNs found in bbpBlue. Interpolating anyway. 24 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_decim.nc... Copied to /mbari/AUVCTD/surveys/2019/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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); length(v_esecs(gindx)) = which is less than 2. Not processing. adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2019_196_04_196_04.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.kml... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_196_04_196_04_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 445) In build_auv_survey (line 530) In AUVprocess_main (line 257)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 2 NaNs found in bbpBlue. Interpolating anyway. 24 NaNs found in bbpRed. Interpolating anyway. Encountered 3938 NaN values in array of lon that is 65864 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 61926 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 61926 are not equal to number of Lat lon points = 65864 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.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.txt... Copied to /mbari/AUVCTD/surveys/2019/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2019/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.nc... Copied to /mbari/AUVCTD/surveys/2019/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04_gridded.mat... Copied to /mbari/AUVCTD/surveys/2019/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_196_04_196_04.mat... Copied to /mbari/AUVCTD/surveys/2019/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2019/netcdf/Dorado389_2019_196_04_196_04.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2019_196_04_196_04 processed" auvctd@listserver.mbari.org < mail_Dorado389_2019_196_04_196_04.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019.196.04.mat Processing time: 311 seconds