Execution of AUVprocess_main version 1.88 at 2025-01-09T20:41:46Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2025, ['008.00'], '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: 2025.008.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/
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/2025/2025008/2025.008.00/navigation.nc')
Creating vector time with 460870 elements.
Creating vector mPos_x with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mPos_y with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mDepth with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mGpsNorth with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mGpsEast with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mGpsValid with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mPhi with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mTheta with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mPsi with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mOmega_x with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mOmega_y with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mOmega_z with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mPsaRange with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mAltitude with 460870 elements.
Creating vector time with 460870 elements.
Creating vector multibeamAltitude with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mDvlAltitude with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mEchoAltitude with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mEchoHorizRange with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mEchoAltitudeLast with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mEchoHorizRangeLast with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mEchoNumOfPings with 460870 elements.
Creating vector time with 460870 elements.
Creating vector nadirCnts with 460870 elements.
Creating vector time with 460870 elements.
Creating vector obstacleCnts with 460870 elements.
Creating vector time with 460870 elements.
Creating vector nGoodNadirBeams with 460870 elements.
Creating vector time with 460870 elements.
Creating vector medianNadirBeamNo with 460870 elements.
Creating vector time with 460870 elements.
Creating vector minBeamRange with 460870 elements.
Creating vector time with 460870 elements.
Creating vector minBeamCnts with 460870 elements.
Creating vector time with 460870 elements.
Creating vector thetaB with 460870 elements.
Creating vector time with 460870 elements.
Creating vector lsAlt with 460870 elements.
Creating vector time with 460870 elements.
Creating vector obstacleSlopeAlt with 460870 elements.
Creating vector time with 460870 elements.
Creating vector obstacleSlopeRange with 460870 elements.
Creating vector time with 460870 elements.
Creating vector obstacleAltAll with 460870 elements.
Creating vector time with 460870 elements.
Creating vector obstacleRangeAll with 460870 elements.
Creating vector time with 460870 elements.
Creating vector flightPathAngle with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mWaterSpeed with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mDvlValid with 460870 elements.
Creating vector time with 460870 elements.
Creating vector multibeamValid with 460870 elements.
Creating vector time with 460870 elements.
Creating vector multibeamFailed with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mDvlNewData with 460870 elements.
Creating vector time with 460870 elements.
Creating vector mDeltaT with 460870 elements.
Creating vector time with 460870 elements.
Creating vector nfix with 460870 elements.
Creating vector time with 460870 elements.
Creating vector efix with 460870 elements.
Creating vector time with 460870 elements.
Creating vector filter_north with 460870 elements.
Creating vector time with 460870 elements.
Creating vector filter_east with 460870 elements.
Creating vector time with 460870 elements.
Creating vector filter_depth with 460870 elements.
Creating vector time with 460870 elements.
Creating vector north_current with 460870 elements.
Creating vector time with 460870 elements.
Creating vector east_current with 460870 elements.
Creating vector time with 460870 elements.
Creating vector speed_bias with 460870 elements.
Creating vector time with 460870 elements.
Creating vector heading_bias with 460870 elements.
Creating vector time with 460870 elements.
Creating vector latitudeNav with 460870 elements.
Creating vector time with 460870 elements.
Creating vector longitudeNav with 460870 elements.
Creating vector time with 460870 elements.
Creating vector dNorthingTrn with 460870 elements.
Creating vector time with 460870 elements.
Creating vector dEastingTrn with 460870 elements.
Creating vector time with 460870 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/navigation.nc');
processNav(): median of positive valued depths = 48.3363
processNav(): Finding depths less than 483.3626 and times > 0
processNav(): length(Nav.depth) = 460870
processNav(): length(gindx)     = 460870
 
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/2025/2025008/2025.008.00/gps.nc')
Creating vector time with 12923 elements.
Creating vector hours with 12923 elements.
Creating vector time with 12923 elements.
Creating vector minutes with 12923 elements.
Creating vector time with 12923 elements.
Creating vector seconds with 12923 elements.
Creating vector time with 12923 elements.
Creating vector centiSeconds with 12923 elements.
Creating vector time with 12923 elements.
Creating vector latitude with 12923 elements.
Creating vector time with 12923 elements.
Creating vector longitude with 12923 elements.
Creating vector time with 12923 elements.
Creating vector quality with 12923 elements.
Creating vector time with 12923 elements.
Creating vector numberOfSatellites with 12923 elements.
Creating vector time with 12923 elements.
Creating vector hdop with 12923 elements.
Creating vector time with 12923 elements.
Creating vector antennaHeight with 12923 elements.
Creating vector time with 12923 elements.
Creating vector geoHeight with 12923 elements.
Creating vector time with 12923 elements.
Creating vector dgpsDataAge with 12923 elements.
Creating vector time with 12923 elements.
Creating vector dgpsRSID with 12923 elements.
Creating vector time with 12923 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/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/2025/2025008/2025.008.00/parosci.nc')
Creating vector time with 917696 elements.
Creating vector depth with 917696 elements.
Creating vector time with 917696 elements.
Creating vector temp with 917696 elements.
Creating vector time with 917696 elements.
Creating vector pressure with 917696 elements.
Creating vector time with 917696 elements.
Creating vector temp_period with 917696 elements.
Creating vector time with 917696 elements.
Creating vector pres_period with 917696 elements.
Creating vector time with 917696 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.23611 max(Depth.data) = 203.0388
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.23611 max(Depth.data) = 203.0388
 
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/2025/2025008/2025.008.00/hydroscatlog.nc')
Creating vector time with 368659 elements.
Creating vector Seconds with 368659 elements.
Creating vector time with 368659 elements.
Creating vector HundrethsOfSeconds with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Snorm1 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Snorm2 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Snorm3 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Gain_Status_1 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Gain_Status_2 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Gain_Status_3 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector RawDepthValue with 368659 elements.
Creating vector time with 368659 elements.
Creating vector RawTempValue with 368659 elements.
Creating vector time with 368659 elements.
Creating vector Temperature with 368659 elements.
Creating vector time with 368659 elements.
Creating vector ErrorValue with 368659 elements.
Creating vector time with 368659 elements.
Creating vector bb470 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector bb676 with 368659 elements.
Creating vector time with 368659 elements.
Creating vector fl676u with 368659 elements.
Creating vector time with 368659 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/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/2025/2025008/2025.008.00/ctdDriver.nc')
Creating vector time with 368785 elements.
Creating vector conductivity with 368785 elements.
Creating vector time with 368785 elements.
Creating vector temperature with 368785 elements.
Creating vector time with 368785 elements.
Creating vector cond_frequency with 368785 elements.
Creating vector time with 368785 elements.
Creating vector temp_frequency with 368785 elements.
Creating vector time with 368785 elements.
Creating vector spare with 368785 elements.
Creating vector time with 368785 elements.
Creating vector humidity with 368785 elements.
Creating vector time with 368785 elements.
Creating vector flow1 with 368785 elements.
Creating vector time with 368785 elements.
Creating vector CDOM with 368785 elements.
Creating vector time with 368785 elements.
Creating vector dissolvedO2 with 368785 elements.
Creating vector time with 368785 elements.
Creating vector salinity with 368785 elements.
Creating vector time with 368785 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/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/2025/2025008/2025.008.00/ctdDriver2.nc')
Creating vector time with 368656 elements.
Creating vector conductivity with 368656 elements.
Creating vector time with 368656 elements.
Creating vector temperature with 368656 elements.
Creating vector time with 368656 elements.
Creating vector cond_frequency with 368656 elements.
Creating vector time with 368656 elements.
Creating vector temp_frequency with 368656 elements.
Creating vector time with 368656 elements.
Creating vector flow2 with 368656 elements.
Creating vector time with 368656 elements.
Creating vector par with 368656 elements.
Creating vector time with 368656 elements.
Creating vector spare with 368656 elements.
Creating vector time with 368656 elements.
Creating vector salinity with 368656 elements.
Creating vector time with 368656 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/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/2025/2025008/2025.008.00/isuslog.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/2025/2025008/2025.008.00/isuslog.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/2025/2025008/2025.008.00/isuslog.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/2025/2025008/2025.008.00/isuslog.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 ISUS structure to NaN values.
 
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/2025/2025008/2025.008.00/biolume.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/2025/2025008/2025.008.00/biolume.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/2025/2025008/2025.008.00/biolume.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/2025/2025008/2025.008.00/biolume.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.


Could not read from biolume.nc returning NaNs for fields.
 
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/2025/2025008/2025.008.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (8782 x 994) with 8729308 elements.
Creating vector time with 8782 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (8782 x 994) with 8729308 elements.
Creating vector time with 8782 elements.
Creating vector bin with 994 elements.
Creating matrix countList (8782 x 994) with 8729308 elements.
Creating vector time with 8782 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 8782 elements.
Creating vector time with 8782 elements.
Creating vector transCount with 8782 elements.
Creating vector time with 8782 elements.
Creating vector nonTransCount with 8782 elements.
Creating vector time with 8782 elements.
Creating vector ai_mean with 8782 elements.
Creating vector time with 8782 elements.
Creating vector ai_min with 8782 elements.
Creating vector time with 8782 elements.
Creating vector ai_max with 8782 elements.
Creating vector time with 8782 elements.
Creating vector ai_std with 8782 elements.
Creating vector time with 8782 elements.
Creating vector esd_mean with 8782 elements.
Creating vector time with 8782 elements.
Creating vector esd_min with 8782 elements.
Creating vector time with 8782 elements.
Creating vector esd_max with 8782 elements.
Creating vector time with 8782 elements.
Creating vector esd_std with 8782 elements.
Creating vector time with 8782 elements.
Creating vector countSum with 8782 elements.
Creating vector time with 8782 elements.
Creating vector snapshot with 8782 elements.
Creating vector time with 8782 elements.
Creating vector threshold with 8782 elements.
Creating vector time with 8782 elements.
Creating vector sampleCount with 8782 elements.
Creating vector time with 8782 elements.
Creating vector flowCount with 8782 elements.
Creating vector time with 8782 elements.
Creating vector flowTime with 8782 elements.
Creating vector time with 8782 elements.
Creating vector bufferStatus with 8782 elements.
Creating vector time with 8782 elements.
Creating vector laserLevel with 8782 elements.
Creating vector time with 8782 elements.
Creating vector counter with 8782 elements.
Creating vector time with 8782 elements.
Creating vector counterPeriod with 8782 elements.
Creating vector time with 8782 elements.
Creating vector laserControl with 8782 elements.
Creating vector time with 8782 elements.
Creating vector countUnknownFrameCharacter with 8782 elements.
Creating vector time with 8782 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 8782 elements.
Creating vector time with 8782 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 8782 elements.
Creating vector time with 8782 elements.
Creating vector flowSpeed with 8782 elements.
Creating vector time with 8782 elements.
Creating vector countShortLFrameError with 8782 elements.
Creating vector time with 8782 elements.
Creating vector countGarbledLFrame with 8782 elements.
Creating vector time with 8782 elements.
Creating vector cFrameEsecs with 8782 elements.
Creating vector time with 8782 elements.
Creating vector correctedSampleCountList with 8782 elements.
Creating vector time with 8782 elements.
Creating vector time with 8782 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025008/2025.008.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.008.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc
*************************************************************************
 
 
*************************************************************************
Calling build_auv_survey.m to construct survey file...
Reading: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.008.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 29 segments.
[Warning: MATLAB has disabled some advanced graphics rendering features by
switching to software OpenGL. For more information, click <a
href="matlab:opengl('problems')">here</a>.] 
Current plot held
Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_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 = 374 Gridding with nix = 1122, 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
Only one good point - NaNing the gN array.
   BL
Only one good point or fewer - NaNing the gBL array.
   BLflow
Only one good point or fewer - NaNing the gBLflow array.
   LOPC
     count
     transCount
     nonTransCount
     LCcount
 
Masking and filtering with median filter of size 5...
  cvarname = gT
  cvarname = gS
  cvarname = gO
  cvarname = gN
No valid data for gN
  cvarname = gF
  cvarname = gB420
  cvarname = gB700
  cvarname = gBL
No valid data for gBL
  cvarname = gBLflow
No valid data for gBLflow
  cvarname = gLOPCcount
  cvarname = gLOPCtransCount
  cvarname = gLOPCnonTransCount
  cvarname = gLOPCLCcount
Encountered 0 NaN values in array of lon that is 430232 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 <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 430232 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2025008_GulperTimes.txt && touch ../results/2025008_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/2025/2025008/2025.008.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2025/2025008/2025.008.00/syslog -startEsecs 1736352485.436 -surveyName Dorado389_2025_008_00_008_00 >> ../results/2025008_GulperTimes.txt
Executing: removeGulpDups.py ../results/2025008_GulperTimes.txt
Bottle: 0 Time: 1736393149.8303 Depth: 200.0201 Dist: 52.1581
Bottle: 1 Time: 1736393303.6298 Depth: 149.9456 Dist: 52.324
Bottle: 2 Time: 1736393562.832 Depth: 59.9708 Dist: 52.621
Bottle: 3 Time: 1736393662.4352 Depth: 29.9966 Dist: 52.7252
Bottle: 4 Time: 1736393700.2326 Depth: 19.9825 Dist: 52.7661
Bottle: 5 Time: 1736393739.4299 Depth: 9.9932 Dist: 52.8082
Bottle: 6 Time: 1736393786.8267 Depth: -0.09429 Dist: 52.8466
Bottle: 7 Time: 1736420733.0307 Depth: 200.0039 Dist: 86.9639
Bottle: 8 Time: 1736420882.2305 Depth: 149.9174 Dist: 87.133
Bottle: 9 Time: 1736421119.0343 Depth: 59.9801 Dist: 87.405
Bottle: 10 Time: 1736421203.0285 Depth: 29.9869 Dist: 87.4958
Bottle: 11 Time: 1736421245.4356 Depth: 19.9549 Dist: 87.5455
Bottle: 12 Time: 1736421280.2332 Depth: 9.9587 Dist: 87.5843
Bottle: 13 Time: 1736421321.4304 Depth: -0.054739 Dist: 87.6249
Bottle: 14 Time: 1736436222.0296 Depth: 150.0683 Dist: 106.1517
Bottle: 15 Time: 1736436462.4332 Depth: 59.9579 Dist: 106.4273
Bottle: 16 Time: 1736436548.8273 Depth: 29.9156 Dist: 106.5246
Bottle: 17 Time: 1736436591.8343 Depth: 19.9551 Dist: 106.5727
Bottle: 18 Time: 1736436636.2313 Depth: 9.9632 Dist: 106.6238
Bottle: 19 Time: 1736436677.0285 Depth: -0.04375 Dist: 106.6674
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_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_2025_008_00_008_00_2column.png
Elapsed time to save image: 10 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_2025_008_00_008_00_biolume.png
Elapsed time to save image: 44 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_2025_008_00_008_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.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00_2column.png...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_biolume.png...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_lopc.png...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_nav_adjust.png...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_hist_stats.png...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_prof_stats.png...
Copied to /mbari/AUVCTD/surveys/2025/images/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
 
*************************************************************************
Writing decimated netCDF file ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2025-01-08T16:08:05Z
gmtstr(tend) = 2025-01-09T17:44:19Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
9 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_2025_008_00_008_00_decim.nc...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Temperature.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Salinity.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Nitrate.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Oxygen.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Optical_Backscatter_420_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Optical_Backscatter_700_nm.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Chlorophyll_Fluorescence.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
length(v_esecs(gindx)) =   which is less than 2.  Not processing.
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_Bioluminescence.kmz...
Copied to /mbari/AUVCTD/surveys/2025/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);
updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_008_00_008_00_LOPC_Total_Count.kmz...
Copied to /mbari/AUVCTD/surveys/2025/kml/.  Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/
 
Creating Dorado389_2025_008_00_008_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00.kml...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_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_2025_008_00_008_00.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2025-01-08T16:08:05Z
gmtstr(tend) = 2025-01-09T17:44:19Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
2 NaNs found in bbpBlue.  Interpolating anyway.
9 NaNs found in bbpRed.  Interpolating anyway.
Encountered 3065 NaN values in array of lon that is 46088 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 <n>f or <n>d, with w to indicate swab
grdtrack: Processing input grid(s)
grdtrack: Output 1 columns via binary records using format f
grdtrack: Sampled 43023 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 43023 are not equal to number of Lat lon points = 46088
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_2025_008_00_008_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_008_00_008_00.txt...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_Gulper.txt...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00.nc...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00_gridded.mat...
Copied to /mbari/AUVCTD/surveys/2025/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_2025_008_00_008_00.mat...
Copied to /mbari/AUVCTD/surveys/2025/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/2025/netcdf/Dorado389_2025_008_00_008_00.nc
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2025_008_00_008_00 processed" mccann@mbari.org < mail_Dorado389_2025_008_00_008_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.008.00.mat
Processing time: 211 seconds