===2023-07-12 00:35:03.167287===
Command: quick_adcp.py --cntfile /mnt/kolea1/uhdas_data_archive/bshimada/SH1800_legs/SH1800_edited/reproc/os75nb/q_py.cnt --auto
Std Output:
initializing cachefile dbinfo.txt
no dbinfo.txt: initializing
fix file is aship.gps
reflayer: ref_method = refsm
reflayer: refuv_source = nav
reflayer: refuv_smoothwin = 3
=====================================================
=====================================================
command line was: /usr/local/bin/quick_adcp.py --cntfile /mnt/kolea1/uhdas_data_archive/bshimada/SH1800_legs/SH1800_edited/reproc/os75nb/q_py.cnt --auto
cwd is /mnt/kolea1/uhdas_data_archive/bshimada/SH1800_legs/SH1800_edited/reproc/os75nb
about to run these steps:
 - write_clearflags
 - update_gbin
 - scandata
 - avg_and_load
 - codaseditsetup
 - setflags
 - getnav
 - lst_hdg
 - plot_headcorr
 - navsteps
 - lst_temp
 - plot_temp
 - lst_npings
 - calib
 - matfiles
 - adcpsect
 - refabs
 - smoothnav
 - putnav
 - refplots
 - codaseditsetup
found 15 files using wildcard expansion relative to scan directory
wildcard string was:   "/mnt/kolea1/uhdas_data_archive/bshimada/SH1800_legs/SH1800_edited/raw/os75/*.raw"
presently in scan, writing filelist to /mnt/kolea1/uhdas_data_archive/bshimada/SH1800_legs/SH1800_edited/reproc/os75nb/ping/datafile_list.txt
found 15 raw data files
---------------------------------------------
step 1: set up files in "edit" directory 

... wrote edit/clearflags.tmp
---------------------------------------------
step 2: generate gbins

---------------------------------------------
step 3: scan files for time range

no database found: starting from scratch
---------------------------------------------
step 4: generate averaged data...
... made file load/ping_editparams.txt
----------------
sonar is os75nb
Pingavg.run for time range 31.734415 to 32.801191
transducer offset: xducer_dx = 0.000, xducer_dy = 0.000
shifted positions applied to *.gpst2 and *.uvship'
----------------
./ens_blk001.cmd  2018/02/01 17:42:32 2018/02/02 17:23:11    31.73788   32.72444
./ens_blk002.cmd  2018/02/02 17:39:36 2018/02/02 19:09:36    32.73583   32.79833
batch    32.79487287    32.79834509  18 1  sh2018_032_64800
Wrote bin, cmd for 305 ensembles in 2 files.  47 seconds
---------------------------------------------
step 5: load averaged data (to database)
3 block files present
database time range:
2018/02/01  17:42:32 to 2018/02/02  19:09:36
(31.737870 to 32.798333)
---------------------------------------------
step 6: set up files for codas editing (gautoedit.py)

... wrote edit/codas_editparams.txt
---------------------------------------------
step 7: run setflags?

---------------------------------------------
step 8: get navigation

navigation file nav/aship.gps created from load/*.gps2
navigation file nav/aship.agt created from load/*.gpst2
plotted  uvship
---------------------------------------------
step 9: list heading

... headings extracted
---------------------------------------------
step 10: plot heading correction

plots are in cal/rotate/*png

-------------------------
---- running navsteps ---
-------------------------
step 11: nav steps: run adcpsect
navstep 1
... ran adcpsect for navsteps
-------------------------
step 12: nav steps: run refabs
navstep 2
... ran refabs for navsteps
-------------------------
step 13: nav steps: run smoothr for plots
navstep 3
... ran smoothr
-------------------------
step 14: nav steps: smooth navigation for velocities
navstep 4
smoothing method for ship speed: refsm
   smoothing window: 3
   ship speed source: nav
... shipspeed smoothing step done
-------------------------
step 15: nav steps: put positions and uvship from refsm into codasdb 
navstep 5
... ran put_txy
... ran put_tuv
... made navigation plot
-------------------------
step 16: nav steps: make reflayer plots
navstep 6
... made reflayer plots
---------------------------------------------
step 11: run calibration steps 

...bottom track info in check cal/botmtrk
... watertrack info in cal/watertrk
... check cal/watertrk for estimate
---------------------------------------------
step 12: extract and plot temperature 

plotted temperature
---------------------------------------------
step 13: extract and plot number of pings per ensemble 

... plotted number of pings per ensemble
---------------------------------------------
step 14: extract matlab "allbins" 

---------------------------------------------
writing "cruise_info.txt"