Execution of AUVprocess_main version 1.88 at 2025-05-21T16:11:02Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2025, ['139.04'], '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: 2025.139.04
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/
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/2025/2025139/2025.139.04/navigation.nc')
Creating vector time with 439445 elements.
Creating vector mPos_x with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mPos_y with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mDepth with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mGpsNorth with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mGpsEast with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mGpsValid with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mPhi with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mTheta with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mPsi with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mOmega_x with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mOmega_y with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mOmega_z with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mPsaRange with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mAltitude with 439445 elements.
Creating vector time with 439445 elements.
Creating vector multibeamAltitude with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mDvlAltitude with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mEchoAltitude with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mEchoHorizRange with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mEchoAltitudeLast with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mEchoHorizRangeLast with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mEchoNumOfPings with 439445 elements.
Creating vector time with 439445 elements.
Creating vector nadirCnts with 439445 elements.
Creating vector time with 439445 elements.
Creating vector obstacleCnts with 439445 elements.
Creating vector time with 439445 elements.
Creating vector nGoodNadirBeams with 439445 elements.
Creating vector time with 439445 elements.
Creating vector medianNadirBeamNo with 439445 elements.
Creating vector time with 439445 elements.
Creating vector minBeamRange with 439445 elements.
Creating vector time with 439445 elements.
Creating vector minBeamCnts with 439445 elements.
Creating vector time with 439445 elements.
Creating vector thetaB with 439445 elements.
Creating vector time with 439445 elements.
Creating vector lsAlt with 439445 elements.
Creating vector time with 439445 elements.
Creating vector obstacleSlopeAlt with 439445 elements.
Creating vector time with 439445 elements.
Creating vector obstacleSlopeRange with 439445 elements.
Creating vector time with 439445 elements.
Creating vector obstacleAltAll with 439445 elements.
Creating vector time with 439445 elements.
Creating vector obstacleRangeAll with 439445 elements.
Creating vector time with 439445 elements.
Creating vector flightPathAngle with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mWaterSpeed with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mDvlValid with 439445 elements.
Creating vector time with 439445 elements.
Creating vector multibeamValid with 439445 elements.
Creating vector time with 439445 elements.
Creating vector multibeamFailed with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mDvlNewData with 439445 elements.
Creating vector time with 439445 elements.
Creating vector mDeltaT with 439445 elements.
Creating vector time with 439445 elements.
Creating vector nfix with 439445 elements.
Creating vector time with 439445 elements.
Creating vector efix with 439445 elements.
Creating vector time with 439445 elements.
Creating vector filter_north with 439445 elements.
Creating vector time with 439445 elements.
Creating vector filter_east with 439445 elements.
Creating vector time with 439445 elements.
Creating vector filter_depth with 439445 elements.
Creating vector time with 439445 elements.
Creating vector north_current with 439445 elements.
Creating vector time with 439445 elements.
Creating vector east_current with 439445 elements.
Creating vector time with 439445 elements.
Creating vector speed_bias with 439445 elements.
Creating vector time with 439445 elements.
Creating vector heading_bias with 439445 elements.
Creating vector time with 439445 elements.
Creating vector latitudeNav with 439445 elements.
Creating vector time with 439445 elements.
Creating vector longitudeNav with 439445 elements.
Creating vector time with 439445 elements.
Creating vector dNorthingTrn with 439445 elements.
Creating vector time with 439445 elements.
Creating vector dEastingTrn with 439445 elements.
Creating vector time with 439445 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/navigation.nc');
processNav(): median of positive valued depths = 46.7694
processNav(): Finding depths less than 467.6944 and times > 0
processNav(): length(Nav.depth) = 439445
processNav(): length(gindx)     = 439445
 
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/2025/2025139/2025.139.04/gps.nc')
Creating vector time with 8975 elements.
Creating vector hours with 8975 elements.
Creating vector time with 8975 elements.
Creating vector minutes with 8975 elements.
Creating vector time with 8975 elements.
Creating vector seconds with 8975 elements.
Creating vector time with 8975 elements.
Creating vector centiSeconds with 8975 elements.
Creating vector time with 8975 elements.
Creating vector latitude with 8975 elements.
Creating vector time with 8975 elements.
Creating vector longitude with 8975 elements.
Creating vector time with 8975 elements.
Creating vector quality with 8975 elements.
Creating vector time with 8975 elements.
Creating vector numberOfSatellites with 8975 elements.
Creating vector time with 8975 elements.
Creating vector hdop with 8975 elements.
Creating vector time with 8975 elements.
Creating vector antennaHeight with 8975 elements.
Creating vector time with 8975 elements.
Creating vector geoHeight with 8975 elements.
Creating vector time with 8975 elements.
Creating vector dgpsDataAge with 8975 elements.
Creating vector time with 8975 elements.
Creating vector dgpsRSID with 8975 elements.
Creating vector time with 8975 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/parosci.nc')
Creating vector time with 875064 elements.
Creating vector depth with 875064 elements.
Creating vector time with 875064 elements.
Creating vector temp with 875064 elements.
Creating vector time with 875064 elements.
Creating vector pressure with 875064 elements.
Creating vector time with 875064 elements.
Creating vector temp_period with 875064 elements.
Creating vector time with 875064 elements.
Creating vector pres_period with 875064 elements.
Creating vector time with 875064 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.32658 max(Depth.data) = 202.931
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.32658 max(Depth.data) = 202.931
 
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/2025/2025139/2025.139.04/hydroscatlog.nc')
Creating vector time with 351535 elements.
Creating vector Seconds with 351535 elements.
Creating vector time with 351535 elements.
Creating vector HundrethsOfSeconds with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Snorm1 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Snorm2 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Snorm3 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Gain_Status_1 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Gain_Status_2 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Gain_Status_3 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector RawDepthValue with 351535 elements.
Creating vector time with 351535 elements.
Creating vector RawTempValue with 351535 elements.
Creating vector time with 351535 elements.
Creating vector Temperature with 351535 elements.
Creating vector time with 351535 elements.
Creating vector ErrorValue with 351535 elements.
Creating vector time with 351535 elements.
Creating vector bb470 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector bb676 with 351535 elements.
Creating vector time with 351535 elements.
Creating vector fl676u with 351535 elements.
Creating vector time with 351535 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/ctdDriver.nc')
Creating vector time with 351650 elements.
Creating vector conductivity with 351650 elements.
Creating vector time with 351650 elements.
Creating vector temperature with 351650 elements.
Creating vector time with 351650 elements.
Creating vector cond_frequency with 351650 elements.
Creating vector time with 351650 elements.
Creating vector temp_frequency with 351650 elements.
Creating vector time with 351650 elements.
Creating vector spare with 351650 elements.
Creating vector time with 351650 elements.
Creating vector humidity with 351650 elements.
Creating vector time with 351650 elements.
Creating vector flow1 with 351650 elements.
Creating vector time with 351650 elements.
Creating vector CDOM with 351650 elements.
Creating vector time with 351650 elements.
Creating vector dissolvedO2 with 351650 elements.
Creating vector time with 351650 elements.
Creating vector salinity with 351650 elements.
Creating vector time with 351650 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/ctdDriver2.nc')
Creating vector time with 351649 elements.
Creating vector conductivity with 351649 elements.
Creating vector time with 351649 elements.
Creating vector temperature with 351649 elements.
Creating vector time with 351649 elements.
Creating vector cond_frequency with 351649 elements.
Creating vector time with 351649 elements.
Creating vector temp_frequency with 351649 elements.
Creating vector time with 351649 elements.
Creating vector flow2 with 351649 elements.
Creating vector time with 351649 elements.
Creating vector par with 351649 elements.
Creating vector time with 351649 elements.
Creating vector spare with 351649 elements.
Creating vector time with 351649 elements.
Creating vector salinity with 351649 elements.
Creating vector time with 351649 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/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/2025/2025139/2025.139.04/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (8374 x 994) with 8323756 elements.
Creating vector time with 8374 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (8374 x 994) with 8323756 elements.
Creating vector time with 8374 elements.
Creating vector bin with 994 elements.
Creating matrix countList (8374 x 994) with 8323756 elements.
Creating vector time with 8374 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 8374 elements.
Creating vector time with 8374 elements.
Creating vector transCount with 8374 elements.
Creating vector time with 8374 elements.
Creating vector nonTransCount with 8374 elements.
Creating vector time with 8374 elements.
Creating vector ai_mean with 8374 elements.
Creating vector time with 8374 elements.
Creating vector ai_min with 8374 elements.
Creating vector time with 8374 elements.
Creating vector ai_max with 8374 elements.
Creating vector time with 8374 elements.
Creating vector ai_std with 8374 elements.
Creating vector time with 8374 elements.
Creating vector esd_mean with 8374 elements.
Creating vector time with 8374 elements.
Creating vector esd_min with 8374 elements.
Creating vector time with 8374 elements.
Creating vector esd_max with 8374 elements.
Creating vector time with 8374 elements.
Creating vector esd_std with 8374 elements.
Creating vector time with 8374 elements.
Creating vector countSum with 8374 elements.
Creating vector time with 8374 elements.
Creating vector snapshot with 8374 elements.
Creating vector time with 8374 elements.
Creating vector threshold with 8374 elements.
Creating vector time with 8374 elements.
Creating vector sampleCount with 8374 elements.
Creating vector time with 8374 elements.
Creating vector flowCount with 8374 elements.
Creating vector time with 8374 elements.
Creating vector flowTime with 8374 elements.
Creating vector time with 8374 elements.
Creating vector bufferStatus with 8374 elements.
Creating vector time with 8374 elements.
Creating vector laserLevel with 8374 elements.
Creating vector time with 8374 elements.
Creating vector counter with 8374 elements.
Creating vector time with 8374 elements.
Creating vector counterPeriod with 8374 elements.
Creating vector time with 8374 elements.
Creating vector laserControl with 8374 elements.
Creating vector time with 8374 elements.
Creating vector countUnknownFrameCharacter with 8374 elements.
Creating vector time with 8374 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 8374 elements.
Creating vector time with 8374 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 8374 elements.
Creating vector time with 8374 elements.
Creating vector flowSpeed with 8374 elements.
Creating vector time with 8374 elements.
Creating vector countShortLFrameError with 8374 elements.
Creating vector time with 8374 elements.
Creating vector countGarbledLFrame with 8374 elements.
Creating vector time with 8374 elements.
Creating vector cFrameEsecs with 8374 elements.
Creating vector time with 8374 elements.
Creating vector correctedSampleCountList with 8374 elements.
Creating vector time with 8374 elements.
Creating vector time with 8374 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025139/2025.139.04/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.139.04.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_2025.139.04.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_139_04_139_04_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_04.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_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 = 382 Gridding with nix = 1146, 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 426439 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 426439 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2025139_GulperTimes.txt && touch ../results/2025139_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/2025/2025139/2025.139.04/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2025/2025139/2025.139.04/syslog -startEsecs 1747680778.1858 -surveyName Dorado389_2025_139_04_139_04 >> ../results/2025139_GulperTimes.txt
Executing: removeGulpDups.py ../results/2025139_GulperTimes.txt
Bottle: 0 Time: 1747722358.7773 Depth: 200.0402 Dist: 53.4728
Bottle: 1 Time: 1747722502.1775 Depth: 149.9967 Dist: 53.6288
Bottle: 2 Time: 1747722743.181 Depth: 59.9825 Dist: 53.8942
Bottle: 3 Time: 1747722830.385 Depth: 29.9513 Dist: 53.9921
Bottle: 4 Time: 1747722873.3821 Depth: 19.9822 Dist: 54.0415
Bottle: 5 Time: 1747722915.5792 Depth: 9.9542 Dist: 54.0878
Bottle: 6 Time: 1747722955.9764 Depth: 0.030985 Dist: 54.1231
Bottle: 7 Time: 1747748929.5771 Depth: 200.0296 Dist: 88.8669
Bottle: 8 Time: 1747749073.1773 Depth: 149.9422 Dist: 89.0301
Bottle: 9 Time: 1747749311.3809 Depth: 59.9334 Dist: 89.3096
Bottle: 10 Time: 1747749392.5854 Depth: 29.9552 Dist: 89.4029
Bottle: 11 Time: 1747749437.3823 Depth: 19.9468 Dist: 89.4534
Bottle: 12 Time: 1747749479.7794 Depth: 9.9749 Dist: 89.501
Bottle: 13 Time: 1747749528.976 Depth: 0.24468 Dist: 89.5523
Bottle: 14 Time: 1747763766.9807 Depth: 150.076 Dist: 107.6938
Bottle: 15 Time: 1747764010.984 Depth: 59.9702 Dist: 107.9799
Bottle: 16 Time: 1747764094.9782 Depth: 29.943 Dist: 108.0747
Bottle: 17 Time: 1747764138.7852 Depth: 19.9861 Dist: 108.1237
Bottle: 18 Time: 1747764180.3824 Depth: 9.9652 Dist: 108.1698
Bottle: 19 Time: 1747764228.1791 Depth: -0.0046198 Dist: 108.2217
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_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_2025_139_04_139_04_2column.png
Elapsed time to save image: 8 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_139_04_139_04_biolume.png
Elapsed time to save image: 29 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_139_04_139_04_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_139_04_139_04_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_04_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_04_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_139_04_139_04_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_139_04_139_04_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_139_04_139_04_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_139_04_139_04_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_139_04_139_04_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) = 2025-05-19T18:52:58Z
gmtstr(tend) = 2025-05-20T19:17:48Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
6 NaNs found in bbpBlue.  Interpolating anyway.
29 NaNs found in bbpRed.  Interpolating anyway.
1 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_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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.
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Optical_Backscatter_420_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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.
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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);
  adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_139_04_139_04_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_139_04_139_04.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_04.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_139_04_139_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_2025_139_04_139_04.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2025-05-19T18:52:58Z
gmtstr(tend) = 2025-05-20T19:17:48Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
6 NaNs found in bbpBlue.  Interpolating anyway.
29 NaNs found in bbpRed.  Interpolating anyway.
1 NaNs found in flRed_uncorr.  Interpolating anyway.
Encountered 1302 NaN values in array of lon that is 43946 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 42644 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 42644 are not equal to number of Lat lon points = 43946
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_139_04_139_04.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_04_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_139_04_139_04.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_139_04_139_04_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_139_04_139_04.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_139_04_139_04_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_139_04_139_04.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_139_04_139_04.nc
 
 
*************************************************************************
Composing email to send to auvctd@listserver.mbari.org ...
!mail -s "Survey Dorado389_2025_139_04_139_04 processed" auvctd@listserver.mbari.org < mail_Dorado389_2025_139_04_139_04.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.139.04.mat
Processing time: 219 seconds