Execution of AUVprocess_main version 1.88 at 2025-06-11T21:33:24Z on elvis
Matlab command executed: 
   AUVprocess_main('AUVCTD', 2025, ['161.00'], '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: 2025.161.00
Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/
Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/
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/2025/2025161/2025.161.00/navigation.nc')
Creating vector time with 454216 elements.
Creating vector mPos_x with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mPos_y with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mDepth with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mGpsNorth with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mGpsEast with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mGpsValid with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mPhi with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mTheta with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mPsi with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mOmega_x with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mOmega_y with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mOmega_z with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mPsaRange with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mAltitude with 454216 elements.
Creating vector time with 454216 elements.
Creating vector multibeamAltitude with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mDvlAltitude with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mEchoAltitude with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mEchoHorizRange with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mEchoAltitudeLast with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mEchoHorizRangeLast with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mEchoNumOfPings with 454216 elements.
Creating vector time with 454216 elements.
Creating vector nadirCnts with 454216 elements.
Creating vector time with 454216 elements.
Creating vector obstacleCnts with 454216 elements.
Creating vector time with 454216 elements.
Creating vector nGoodNadirBeams with 454216 elements.
Creating vector time with 454216 elements.
Creating vector medianNadirBeamNo with 454216 elements.
Creating vector time with 454216 elements.
Creating vector minBeamRange with 454216 elements.
Creating vector time with 454216 elements.
Creating vector minBeamCnts with 454216 elements.
Creating vector time with 454216 elements.
Creating vector thetaB with 454216 elements.
Creating vector time with 454216 elements.
Creating vector lsAlt with 454216 elements.
Creating vector time with 454216 elements.
Creating vector obstacleSlopeAlt with 454216 elements.
Creating vector time with 454216 elements.
Creating vector obstacleSlopeRange with 454216 elements.
Creating vector time with 454216 elements.
Creating vector obstacleAltAll with 454216 elements.
Creating vector time with 454216 elements.
Creating vector obstacleRangeAll with 454216 elements.
Creating vector time with 454216 elements.
Creating vector flightPathAngle with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mWaterSpeed with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mDvlValid with 454216 elements.
Creating vector time with 454216 elements.
Creating vector multibeamValid with 454216 elements.
Creating vector time with 454216 elements.
Creating vector multibeamFailed with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mDvlNewData with 454216 elements.
Creating vector time with 454216 elements.
Creating vector mDeltaT with 454216 elements.
Creating vector time with 454216 elements.
Creating vector nfix with 454216 elements.
Creating vector time with 454216 elements.
Creating vector efix with 454216 elements.
Creating vector time with 454216 elements.
Creating vector filter_north with 454216 elements.
Creating vector time with 454216 elements.
Creating vector filter_east with 454216 elements.
Creating vector time with 454216 elements.
Creating vector filter_depth with 454216 elements.
Creating vector time with 454216 elements.
Creating vector north_current with 454216 elements.
Creating vector time with 454216 elements.
Creating vector east_current with 454216 elements.
Creating vector time with 454216 elements.
Creating vector speed_bias with 454216 elements.
Creating vector time with 454216 elements.
Creating vector heading_bias with 454216 elements.
Creating vector time with 454216 elements.
Creating vector latitudeNav with 454216 elements.
Creating vector time with 454216 elements.
Creating vector longitudeNav with 454216 elements.
Creating vector time with 454216 elements.
Creating vector dNorthingTrn with 454216 elements.
Creating vector time with 454216 elements.
Creating vector dEastingTrn with 454216 elements.
Creating vector time with 454216 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/navigation.nc');
processNav(): median of positive valued depths = 47.6431
processNav(): Finding depths less than 476.4314 and times > 0
processNav(): length(Nav.depth) = 454216
processNav(): length(gindx)     = 454216
 
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/2025/2025161/2025.161.00/gps.nc')
Creating vector time with 9776 elements.
Creating vector hours with 9776 elements.
Creating vector time with 9776 elements.
Creating vector minutes with 9776 elements.
Creating vector time with 9776 elements.
Creating vector seconds with 9776 elements.
Creating vector time with 9776 elements.
Creating vector centiSeconds with 9776 elements.
Creating vector time with 9776 elements.
Creating vector latitude with 9776 elements.
Creating vector time with 9776 elements.
Creating vector longitude with 9776 elements.
Creating vector time with 9776 elements.
Creating vector quality with 9776 elements.
Creating vector time with 9776 elements.
Creating vector numberOfSatellites with 9776 elements.
Creating vector time with 9776 elements.
Creating vector hdop with 9776 elements.
Creating vector time with 9776 elements.
Creating vector antennaHeight with 9776 elements.
Creating vector time with 9776 elements.
Creating vector geoHeight with 9776 elements.
Creating vector time with 9776 elements.
Creating vector dgpsDataAge with 9776 elements.
Creating vector time with 9776 elements.
Creating vector dgpsRSID with 9776 elements.
Creating vector time with 9776 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/parosci.nc')
Creating vector time with 904442 elements.
Creating vector depth with 904442 elements.
Creating vector time with 904442 elements.
Creating vector temp with 904442 elements.
Creating vector time with 904442 elements.
Creating vector pressure with 904442 elements.
Creating vector time with 904442 elements.
Creating vector temp_period with 904442 elements.
Creating vector time with 904442 elements.
Creating vector pres_period with 904442 elements.
Creating vector time with 904442 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/parosci.nc');
in processDepth.m
Before: min(Depth.data) = -0.26141 max(Depth.data) = 202.8336
Found 0 bad (> 300 | < -1.0) depth values in Depth.data.  Replacing with NaNs
After: min(Depth.data) = -0.26141 max(Depth.data) = 202.8336
 
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/2025/2025161/2025.161.00/hydroscatlog.nc')
Creating vector time with 363342 elements.
Creating vector Seconds with 363342 elements.
Creating vector time with 363342 elements.
Creating vector HundrethsOfSeconds with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Snorm1 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Snorm2 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Snorm3 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Gain_Status_1 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Gain_Status_2 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Gain_Status_3 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector RawDepthValue with 363342 elements.
Creating vector time with 363342 elements.
Creating vector RawTempValue with 363342 elements.
Creating vector time with 363342 elements.
Creating vector Temperature with 363342 elements.
Creating vector time with 363342 elements.
Creating vector ErrorValue with 363342 elements.
Creating vector time with 363342 elements.
Creating vector bb470 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector bb676 with 363342 elements.
Creating vector time with 363342 elements.
Creating vector fl676u with 363342 elements.
Creating vector time with 363342 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/ctdDriver.nc')
Creating vector time with 363460 elements.
Creating vector conductivity with 363460 elements.
Creating vector time with 363460 elements.
Creating vector temperature with 363460 elements.
Creating vector time with 363460 elements.
Creating vector cond_frequency with 363460 elements.
Creating vector time with 363460 elements.
Creating vector temp_frequency with 363460 elements.
Creating vector time with 363460 elements.
Creating vector spare with 363460 elements.
Creating vector time with 363460 elements.
Creating vector humidity with 363460 elements.
Creating vector time with 363460 elements.
Creating vector flow1 with 363460 elements.
Creating vector time with 363460 elements.
Creating vector CDOM with 363460 elements.
Creating vector time with 363460 elements.
Creating vector dissolvedO2 with 363460 elements.
Creating vector time with 363460 elements.
Creating vector salinity with 363460 elements.
Creating vector time with 363460 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/ctdDriver.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/ctdDriver2.nc')
Creating vector time with 363332 elements.
Creating vector conductivity with 363332 elements.
Creating vector time with 363332 elements.
Creating vector temperature with 363332 elements.
Creating vector time with 363332 elements.
Creating vector cond_frequency with 363332 elements.
Creating vector time with 363332 elements.
Creating vector temp_frequency with 363332 elements.
Creating vector time with 363332 elements.
Creating vector flow2 with 363332 elements.
Creating vector time with 363332 elements.
Creating vector par with 363332 elements.
Creating vector time with 363332 elements.
Creating vector spare with 363332 elements.
Creating vector time with 363332 elements.
Creating vector salinity with 363332 elements.
Creating vector time with 363332 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/ctdDriver2.nc');
Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/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/2025/2025161/2025.161.00/lopc.nc')
Creating vector bin with 994 elements.
Creating matrix sepCountList (8655 x 994) with 8603070 elements.
Creating vector time with 8655 elements.
Creating vector bin with 994 elements.
Creating matrix mepCountList (8655 x 994) with 8603070 elements.
Creating vector time with 8655 elements.
Creating vector bin with 994 elements.
Creating matrix countList (8655 x 994) with 8603070 elements.
Creating vector time with 8655 elements.
Creating vector bin with 994 elements.
Creating vector LCcount with 8655 elements.
Creating vector time with 8655 elements.
Creating vector transCount with 8655 elements.
Creating vector time with 8655 elements.
Creating vector nonTransCount with 8655 elements.
Creating vector time with 8655 elements.
Creating vector ai_mean with 8655 elements.
Creating vector time with 8655 elements.
Creating vector ai_min with 8655 elements.
Creating vector time with 8655 elements.
Creating vector ai_max with 8655 elements.
Creating vector time with 8655 elements.
Creating vector ai_std with 8655 elements.
Creating vector time with 8655 elements.
Creating vector esd_mean with 8655 elements.
Creating vector time with 8655 elements.
Creating vector esd_min with 8655 elements.
Creating vector time with 8655 elements.
Creating vector esd_max with 8655 elements.
Creating vector time with 8655 elements.
Creating vector esd_std with 8655 elements.
Creating vector time with 8655 elements.
Creating vector countSum with 8655 elements.
Creating vector time with 8655 elements.
Creating vector snapshot with 8655 elements.
Creating vector time with 8655 elements.
Creating vector threshold with 8655 elements.
Creating vector time with 8655 elements.
Creating vector sampleCount with 8655 elements.
Creating vector time with 8655 elements.
Creating vector flowCount with 8655 elements.
Creating vector time with 8655 elements.
Creating vector flowTime with 8655 elements.
Creating vector time with 8655 elements.
Creating vector bufferStatus with 8655 elements.
Creating vector time with 8655 elements.
Creating vector laserLevel with 8655 elements.
Creating vector time with 8655 elements.
Creating vector counter with 8655 elements.
Creating vector time with 8655 elements.
Creating vector counterPeriod with 8655 elements.
Creating vector time with 8655 elements.
Creating vector laserControl with 8655 elements.
Creating vector time with 8655 elements.
Creating vector countUnknownFrameCharacter with 8655 elements.
Creating vector time with 8655 elements.
Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 8655 elements.
Creating vector time with 8655 elements.
Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 8655 elements.
Creating vector time with 8655 elements.
Creating vector flowSpeed with 8655 elements.
Creating vector time with 8655 elements.
Creating vector countShortLFrameError with 8655 elements.
Creating vector time with 8655 elements.
Creating vector countGarbledLFrame with 8655 elements.
Creating vector time with 8655 elements.
Creating vector cFrameEsecs with 8655 elements.
Creating vector time with 8655 elements.
Creating vector correctedSampleCountList with 8655 elements.
Creating vector time with 8655 elements.
Creating vector time with 8655 elements.
att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2025/2025161/2025.161.00/lopc.nc');
 
save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.161.00.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_2025.161.00.mat
Calling matchDVLtoGPS to adjust dvl data in the underwater segments...
setting up UTM transformation using M_Map calls...
Looping over 28 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_161_00_161_00_nav_adjust.png
Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_00.mat
Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_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 = 370 Gridding with nix = 1110, 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 438534 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 438534 points from grid Monterey25.grd (2876 x 2447)
Executing: /bin/rm -f ../results/2025161_GulperTimes.txt && touch ../results/2025161_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/2025/2025161/2025.161.00/navigation.nc.ascii?time[0:1:0]
Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2025/2025161/2025.161.00/syslog -startEsecs 1749578132.8029 -surveyName Dorado389_2025_161_00_161_00 >> ../results/2025161_GulperTimes.txt
Executing: removeGulpDups.py ../results/2025161_GulperTimes.txt
Bottle: 0 Time: 1749618847.9937 Depth: 200.0432 Dist: 52.9762
Bottle: 1 Time: 1749618988.1941 Depth: 149.929 Dist: 53.1361
Bottle: 2 Time: 1749619212.1988 Depth: 59.9821 Dist: 53.3927
Bottle: 3 Time: 1749619302.2026 Depth: 29.9209 Dist: 53.4842
Bottle: 4 Time: 1749619337.2002 Depth: 19.9546 Dist: 53.521
Bottle: 5 Time: 1749619371.3979 Depth: 9.9416 Dist: 53.5624
Bottle: 6 Time: 1749619404.1956 Depth: 2.1618 Dist: 53.6087
Bottle: 7 Time: 1749647879.195 Depth: 200.0601 Dist: 90.3187
Bottle: 8 Time: 1749648026.3949 Depth: 149.9945 Dist: 90.4858
Bottle: 9 Time: 1749648266.1984 Depth: 59.9996 Dist: 90.772
Bottle: 10 Time: 1749648350.6026 Depth: 29.9343 Dist: 90.8645
Bottle: 11 Time: 1749648396.9995 Depth: 19.9264 Dist: 90.9155
Bottle: 12 Time: 1749648439.5965 Depth: 9.9344 Dist: 90.9654
Bottle: 13 Time: 1749648489.3931 Depth: 0.15777 Dist: 91.0242
Bottle: 14 Time: 1749663515.5938 Depth: 150.0013 Dist: 109.7664
Bottle: 15 Time: 1749663755.1974 Depth: 59.9297 Dist: 110.0451
Bottle: 16 Time: 1749663839.6016 Depth: 29.9838 Dist: 110.1378
Bottle: 17 Time: 1749663881.7987 Depth: 19.9691 Dist: 110.1872
Bottle: 18 Time: 1749663917.7962 Depth: 9.9328 Dist: 110.2299
Bottle: 19 Time: 1749663957.9935 Depth: 0.13178 Dist: 110.2727
Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_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_161_00_161_00_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_161_00_161_00_biolume.png
Elapsed time to save image: 28 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_161_00_161_00_lopc.png
Elapsed time to save image: 8 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_161_00_161_00_hist_stats.png
Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_00_prof_stats.png
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_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_161_00_161_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_161_00_161_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_161_00_161_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_161_00_161_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_161_00_161_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) = 2025-06-10T17:55:32Z
gmtstr(tend) = 2025-06-11T19:09:36Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
18 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_161_00_161_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_161_00_161_00_Temperature.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Salinity.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Nitrate.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Oxygen.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Optical_Backscatter_420_nm.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Optical_Backscatter_700_nm.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Chlorophyll_Fluorescence.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_Bioluminescence.kml (deflated 94%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00_LOPC_Total_Count.kml (deflated 93%)
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2025_161_00_161_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_161_00_161_00.kml file to hold all the variable .kmz files...
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_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_161_00_161_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_161_00_161_00.mat ...
Iterpolating to 2 second increments between Nav time bounds...
gmtstr(tstart) = 2025-06-10T17:55:32Z
gmtstr(tend) = 2025-06-11T19:09:36Z
Interpolating ctd1 temperature...
Interpolating ctd1 salinity...
18 NaNs found in bbpRed.  Interpolating anyway.
Encountered 1569 NaN values in array of lon that is 45422 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 43853 points from grid Monterey25.grd (2876 x 2447)
Number of depths returned from grdtrack = 43853 are not equal to number of Lat lon points = 45422
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_161_00_161_00.txt
Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_00_Gulper.txt
Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025_161_00_161_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_161_00_161_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_161_00_161_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_161_00_161_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_161_00_161_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_161_00_161_00.nc
 
 
*************************************************************************
Composing email to send to mccann@mbari.org ...
!mail -s "Survey Dorado389_2025_161_00_161_00 processed" mccann@mbari.org < mail_Dorado389_2025_161_00_161_00.txt
Removing mission .mat files:
   /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2025.161.00.mat
Processing time: 183 seconds