Execution of AUVprocess_main version 1.88 at 2021-07-29T18:01:28Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2019, ['176.00'], '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: 2019.176.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/ 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/2019/2019176/2019.176.00/navigation.nc') Creating vector time with 382820 elements. Creating vector mPos_x with 382820 elements. Creating vector time with 382820 elements. Creating vector mPos_y with 382820 elements. Creating vector time with 382820 elements. Creating vector mDepth with 382820 elements. Creating vector time with 382820 elements. Creating vector mGpsNorth with 382820 elements. Creating vector time with 382820 elements. Creating vector mGpsEast with 382820 elements. Creating vector time with 382820 elements. Creating vector mGpsValid with 382820 elements. Creating vector time with 382820 elements. Creating vector mPhi with 382820 elements. Creating vector time with 382820 elements. Creating vector mTheta with 382820 elements. Creating vector time with 382820 elements. Creating vector mPsi with 382820 elements. Creating vector time with 382820 elements. Creating vector mOmega_x with 382820 elements. Creating vector time with 382820 elements. Creating vector mOmega_y with 382820 elements. Creating vector time with 382820 elements. Creating vector mOmega_z with 382820 elements. Creating vector time with 382820 elements. Creating vector mPsaRange with 382820 elements. Creating vector time with 382820 elements. Creating vector mAltitude with 382820 elements. Creating vector time with 382820 elements. Creating vector multibeamAltitude with 382820 elements. Creating vector time with 382820 elements. Creating vector mDvlAltitude with 382820 elements. Creating vector time with 382820 elements. Creating vector mEchoAltitude with 382820 elements. Creating vector time with 382820 elements. Creating vector mEchoHorizRange with 382820 elements. Creating vector time with 382820 elements. Creating vector mEchoAltitudeLast with 382820 elements. Creating vector time with 382820 elements. Creating vector mEchoHorizRangeLast with 382820 elements. Creating vector time with 382820 elements. Creating vector mEchoNumOfPings with 382820 elements. Creating vector time with 382820 elements. Creating vector nadirCnts with 382820 elements. Creating vector time with 382820 elements. Creating vector obstacleCnts with 382820 elements. Creating vector time with 382820 elements. Creating vector nGoodNadirBeams with 382820 elements. Creating vector time with 382820 elements. Creating vector medianNadirBeamNo with 382820 elements. Creating vector time with 382820 elements. Creating vector mWaterSpeed with 382820 elements. Creating vector time with 382820 elements. Creating vector mDvlValid with 382820 elements. Creating vector time with 382820 elements. Creating vector mDvlNewData with 382820 elements. Creating vector time with 382820 elements. Creating vector mDeltaT with 382820 elements. Creating vector time with 382820 elements. Creating vector nfix with 382820 elements. Creating vector time with 382820 elements. Creating vector efix with 382820 elements. Creating vector time with 382820 elements. Creating vector filter_north with 382820 elements. Creating vector time with 382820 elements. Creating vector filter_east with 382820 elements. Creating vector time with 382820 elements. Creating vector filter_depth with 382820 elements. Creating vector time with 382820 elements. Creating vector north_current with 382820 elements. Creating vector time with 382820 elements. Creating vector east_current with 382820 elements. Creating vector time with 382820 elements. Creating vector speed_bias with 382820 elements. Creating vector time with 382820 elements. Creating vector heading_bias with 382820 elements. Creating vector time with 382820 elements. Creating vector latitude with 382820 elements. Creating vector time with 382820 elements. Creating vector longitude with 382820 elements. Creating vector time with 382820 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/navigation.nc'); processNav(): median of positive valued depths = 31.6997 processNav(): Finding depths less than 221.8982 and times > 0 processNav(): length(Nav.depth) = 382820 processNav(): length(gindx) = 382820 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/2019/2019176/2019.176.00/gps.nc') Creating vector time with 14488 elements. Creating vector hours with 14488 elements. Creating vector time with 14488 elements. Creating vector minutes with 14488 elements. Creating vector time with 14488 elements. Creating vector seconds with 14488 elements. Creating vector time with 14488 elements. Creating vector centiSeconds with 14488 elements. Creating vector time with 14488 elements. Creating vector latitude with 14488 elements. Creating vector time with 14488 elements. Creating vector longitude with 14488 elements. Creating vector time with 14488 elements. Creating vector quality with 14488 elements. Creating vector time with 14488 elements. Creating vector numberOfSatellites with 14488 elements. Creating vector time with 14488 elements. Creating vector hdop with 14488 elements. Creating vector time with 14488 elements. Creating vector antennaHeight with 14488 elements. Creating vector time with 14488 elements. Creating vector geoHeight with 14488 elements. Creating vector time with 14488 elements. Creating vector dgpsDataAge with 14488 elements. Creating vector time with 14488 elements. Creating vector dgpsRSID with 14488 elements. Creating vector time with 14488 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/parosci.nc') Creating vector time with 762334 elements. Creating vector depth with 762334 elements. Creating vector time with 762334 elements. Creating vector temp with 762334 elements. Creating vector time with 762334 elements. Creating vector pressure with 762334 elements. Creating vector time with 762334 elements. Creating vector temp_period with 762334 elements. Creating vector time with 762334 elements. Creating vector pres_period with 762334 elements. Creating vector time with 762334 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.62487 max(Depth.data) = 202.8407 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.62487 max(Depth.data) = 202.8407 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/2019/2019176/2019.176.00/hydroscatlog.nc') Creating vector time with 306214 elements. Creating vector Seconds with 306214 elements. Creating vector time with 306214 elements. Creating vector HundrethsOfSeconds with 306214 elements. Creating vector time with 306214 elements. Creating vector Snorm1 with 306214 elements. Creating vector time with 306214 elements. Creating vector Snorm2 with 306214 elements. Creating vector time with 306214 elements. Creating vector Snorm3 with 306214 elements. Creating vector time with 306214 elements. Creating vector Gain_Status_1 with 306214 elements. Creating vector time with 306214 elements. Creating vector Gain_Status_2 with 306214 elements. Creating vector time with 306214 elements. Creating vector Gain_Status_3 with 306214 elements. Creating vector time with 306214 elements. Creating vector RawDepthValue with 306214 elements. Creating vector time with 306214 elements. Creating vector RawTempValue with 306214 elements. Creating vector time with 306214 elements. Creating vector Temperature with 306214 elements. Creating vector time with 306214 elements. Creating vector ErrorValue with 306214 elements. Creating vector time with 306214 elements. Creating vector bb470 with 306214 elements. Creating vector time with 306214 elements. Creating vector bb676 with 306214 elements. Creating vector time with 306214 elements. Creating vector fl676u with 306214 elements. Creating vector time with 306214 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/ctdDriver.nc') Creating vector time with 306225 elements. Creating vector conductivity with 306225 elements. Creating vector time with 306225 elements. Creating vector temperature with 306225 elements. Creating vector time with 306225 elements. Creating vector cond_frequency with 306225 elements. Creating vector time with 306225 elements. Creating vector temp_frequency with 306225 elements. Creating vector time with 306225 elements. Creating vector spare with 306225 elements. Creating vector time with 306225 elements. Creating vector humidity with 306225 elements. Creating vector time with 306225 elements. Creating vector flow1 with 306225 elements. Creating vector time with 306225 elements. Creating vector CDOM with 306225 elements. Creating vector time with 306225 elements. Creating vector dissolvedO2 with 306225 elements. Creating vector time with 306225 elements. Creating vector salinity with 306225 elements. Creating vector time with 306225 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/ctdDriver2.nc') Creating vector time with 306293 elements. Creating vector conductivity with 306293 elements. Creating vector time with 306293 elements. Creating vector temperature with 306293 elements. Creating vector time with 306293 elements. Creating vector cond_frequency with 306293 elements. Creating vector time with 306293 elements. Creating vector temp_frequency with 306293 elements. Creating vector time with 306293 elements. Creating vector flow2 with 306293 elements. Creating vector time with 306293 elements. Creating vector spare with 306293 elements. Creating vector time with 306293 elements. Creating vector salinity with 306293 elements. Creating vector time with 306293 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/isuslog.nc') Creating vector time with 59813 elements. Creating vector isusNitrate with 59813 elements. Creating vector time with 59813 elements. Creating vector isusTemp with 59813 elements. Creating vector time with 59813 elements. Creating vector isusQuality with 59813 elements. Creating vector time with 59813 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/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 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/2019/2019176/2019.176.00/biolume.nc') Creating vector time with 75310 elements. Creating vector rrr with 75310 elements. Creating vector time with 75310 elements. Creating vector cal_striing with 75310 elements. Creating vector time with 75310 elements. Creating vector avg_biolume with 75310 elements. Creating vector time with 75310 elements. Creating vector pump with 75310 elements. Creating vector time with 75310 elements. Creating vector system_voltage with 75310 elements. Creating vector time with 75310 elements. Creating vector flow with 75310 elements. Creating vector time with 75310 elements. Creating vector HV with 75310 elements. Creating vector time with 75310 elements. Creating vector reserved with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_0 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_1 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_2 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_3 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_4 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_5 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_6 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_7 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_8 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_9 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_10 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_11 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_12 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_13 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_14 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_15 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_16 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_17 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_18 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_19 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_20 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_21 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_22 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_23 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_24 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_25 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_26 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_27 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_28 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_29 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_30 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_31 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_32 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_33 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_34 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_35 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_36 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_37 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_38 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_39 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_40 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_41 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_42 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_43 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_44 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_45 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_46 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_47 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_48 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_49 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_50 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_51 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_52 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_53 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_54 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_55 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_56 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_57 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_58 with 75310 elements. Creating vector time with 75310 elements. Creating vector raw_59 with 75310 elements. Creating vector time with 75310 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/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/2019/2019176/2019.176.00/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_2019.176.00.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.cvs/src/matlab/doradosdp/results/Dorado389_2019.176.00.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 33 segments. *** WARNING: no data in dvlSegSurfLat for segment 22. Continuing to next segment Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_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 = 438 Gridding with nix = 1314, iZ = 403 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 372777 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 372777 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: 06/25/2019 09:30 to 06/26/2019 09:30 swr = 345.2484 448.1978 694.0531 750.0264 821.6557 870.6385 806.9164 628.6468 424.1629 232.6748 64.0559 8.8594 1.4252 1.7333 1.6582 1.7336 1.4748 1.6333 1.5583 1.4415 2.8746 66.8161 266.0643 410.4805 674.6005 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2019176_GulperTimes.txt && touch ../results/2019176_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/2019/2019176/2019.176.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2019/2019176/2019.176.00/syslog -startEsecs 1561489082.4345 -surveyName Dorado389_2019_176_00_176_00 >> ../results/2019176_GulperTimes.txt Executing: removeGulpDups.py ../results/2019176_GulperTimes.txt Bottle: 0 Time: 1561490357.8271 Depth: 200.0093 Dist: 1.2072 Bottle: 1 Time: 1561490476.229 Depth: 149.9731 Dist: 1.3457 Bottle: 2 Time: 1561490585.4315 Depth: 99.9339 Dist: 1.4698 Bottle: 3 Time: 1561490633.4283 Depth: 79.9966 Dist: 1.5165 Bottle: 4 Time: 1561490684.0348 Depth: 59.9913 Dist: 1.5704 Bottle: 5 Time: 1561490737.0312 Depth: 39.9608 Dist: 1.637 Bottle: 6 Time: 1561490764.8293 Depth: 29.9585 Dist: 1.6665 Bottle: 7 Time: 1561490794.2272 Depth: 19.9378 Dist: 1.6923 Bottle: 8 Time: 1561490823.0353 Depth: 9.987 Dist: 1.7188 Bottle: 9 Time: 1561490897.2302 Depth: -0.30321 Dist: 1.7742 Bottle: 10 Time: 1561520422.1225 Depth: 200.0458 Dist: 35.8843 Bottle: 11 Time: 1561520542.1243 Depth: 149.9832 Dist: 36.005 Bottle: 12 Time: 1561520653.7266 Depth: 99.9482 Dist: 36.1157 Bottle: 13 Time: 1561520702.7232 Depth: 79.9042 Dist: 36.1624 Bottle: 14 Time: 1561520752.3299 Depth: 59.9479 Dist: 36.2135 Bottle: 15 Time: 1561520804.3999 Depth: 39.9568 Dist: 36.2703 Bottle: 16 Time: 1561520832.798 Depth: 29.9774 Dist: 36.2967 Bottle: 17 Time: 1561520863.7959 Depth: 19.9912 Dist: 36.3183 Bottle: 18 Time: 1561520890.404 Depth: 9.9339 Dist: 36.339 Bottle: 19 Time: 1561520922.4018 Depth: -0.21362 Dist: 36.3748 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_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.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_2column.png Elapsed time to save image: 23 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_176_00_176_00_biolume.png Elapsed time to save image: 53 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_176_00_176_00_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_176_00_176_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_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_176_00_176_00_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_176_00_176_00_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_176_00_176_00_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_176_00_176_00_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_176_00_176_00_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... 4 NaNs found in bbpBlue. Interpolating anyway. 24 NaNs found in bbpRed. Interpolating anyway. 3 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_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_176_00_176_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_176_00_176_00_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_176_00_176_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00.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_176_00_176_00_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_176_00_176_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 4 NaNs found in bbpBlue. Interpolating anyway. 24 NaNs found in bbpRed. Interpolating anyway. 3 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 823 NaN values in array of lon that is 59781 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 58958 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 58958 are not equal to number of Lat lon points = 59781 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_176_00_176_00.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_176_00_176_00.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_176_00_176_00_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_176_00_176_00.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_176_00_176_00_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_176_00_176_00.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_176_00_176_00.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2019_176_00_176_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2019_176_00_176_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019.176.00.mat Processing time: 332 seconds