ERROR 2023-07-07 21:58:08,357 logs2netcdfs.py _unique_vehicle_names():312 [55] Cannot read http://portal.shore.mbari.org:8080/auvdata/v1/deployments, status_code = 404
INFO 2023-07-07 21:58:08,357 logs2netcdfs.py download_process_logs():688 [55] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010181/2010.181.00 to /data/auv_data/dorado/missionlogs/2010.181.00
INFO 2023-07-07 21:58:09,132 logs2netcdfs.py download_process_logs():696 [55] Processing mission: dorado 2010.181.00
INFO 2023-07-07 21:58:09,133 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/ctdDriver.log (544043 bytes)
INFO 2023-07-07 21:58:09,265 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/ctdDriver2.log (544127 bytes)
INFO 2023-07-07 21:58:09,377 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/gps.log (80420 bytes)
INFO 2023-07-07 21:58:09,410 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/hydroscatlog.log (486550 bytes)
INFO 2023-07-07 21:58:09,543 logs2netcdfs.py _process_log_file():644 [55] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.181.00/hydroscatlog.log: [814]
INFO 2023-07-07 21:58:09,546 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/navigation.log (1662982 bytes)
INFO 2023-07-07 21:58:09,862 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/isuslog.log (35797 bytes)
INFO 2023-07-07 21:58:09,876 logs2netcdfs.py _process_log_file():644 [55] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.181.00/isuslog.log: [ 1  2  3  4  5  7  8  9 10 11 12 13 14 15 16 17 18 19]
INFO 2023-07-07 21:58:09,877 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/parosci.log (566359 bytes)
WARNING 2023-07-07 21:58:09,975 logs2netcdfs.py _read_data():206 [55] unpack requires a buffer of 8 bytes, b = b'\n' at record 11792, for temp in file /data/auv_data/dorado/missionlogs/2010.181.00/parosci.log
INFO 2023-07-07 21:58:09,975 logs2netcdfs.py _read_data():210 [55] bytes read = 566366 file size = 566359
INFO 2023-07-07 21:58:09,975 logs2netcdfs.py _read_data():214 [55] Tried to read 8 bytes, but only 7 bytes remaining
INFO 2023-07-07 21:58:09,976 logs2netcdfs.py _read_data():220 [55] Successfully unpacked 11792 records
WARNING 2023-07-07 21:58:09,983 logs2netcdfs.py _create_variable():493 [55] shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (11793,) and arg 1 with shape (11792,).
INFO 2023-07-07 21:58:09,983 logs2netcdfs.py _create_variable():494 [55] len(data) (11792) does not match shape of pressure.shape[0] (11793)
WARNING 2023-07-07 21:58:09,983 logs2netcdfs.py _create_variable():499 [55] pressure data is short by one, appending the last value: -0.017578965222514602
WARNING 2023-07-07 21:58:09,985 logs2netcdfs.py _create_variable():493 [55] shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (11793,) and arg 1 with shape (11792,).
INFO 2023-07-07 21:58:09,985 logs2netcdfs.py _create_variable():494 [55] len(data) (11792) does not match shape of temp_period.shape[0] (11793)
WARNING 2023-07-07 21:58:09,985 logs2netcdfs.py _create_variable():499 [55] temp_period data is short by one, appending the last value: 13.777510219818605
WARNING 2023-07-07 21:58:09,987 logs2netcdfs.py _create_variable():493 [55] shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (11793,) and arg 1 with shape (11792,).
INFO 2023-07-07 21:58:09,988 logs2netcdfs.py _create_variable():494 [55] len(data) (11792) does not match shape of pres_period.shape[0] (11793)
WARNING 2023-07-07 21:58:09,988 logs2netcdfs.py _create_variable():499 [55] pres_period data is short by one, appending the last value: 1.0912982514340954
INFO 2023-07-07 21:58:10,019 logs2netcdfs.py _process_log_file():644 [55] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.181.00/parosci.log: [  154   155   156 ... 11790 11791 11792]
INFO 2023-07-07 21:58:10,022 logs2netcdfs.py download_process_logs():705 [55] Processing file /data/auv_data/dorado/missionlogs/2010.181.00/tailCone.log (346891 bytes)
INFO 2023-07-07 21:58:10,137 logs2netcdfs.py download_process_logs():722 [55] Time to process: 1.00 seconds
INFO 2023-07-07 21:58:10,137 lopcToNetCDF.py main():2282 [55] Processing begun: Fri Jul  7 21:58:10 2023
INFO 2023-07-07 21:58:10,137 lopcToNetCDF.py constructTimestampList():1300 [55] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.181.00/parosci.nc
INFO 2023-07-07 21:58:10,138 lopcToNetCDF.py constructTimestampList():1301 [55] Using NetCDF4 to get start and end epoch seconds for this mission from this URL:
INFO 2023-07-07 21:58:10,138 lopcToNetCDF.py constructTimestampList():1304 [55] /data/auv_data/dorado/missionnetcdfs/2010.181.00/parosci.nc
INFO 2023-07-07 21:58:10,142 lopcToNetCDF.py constructTimestampList():1321 [55] From associated parosci.nc file: sensor_on_time = 1277910796.5, sensor_off_time = 5.8
INFO 2023-07-07 21:58:10,142 lopcToNetCDF.py constructTimestampList():1325 [55] Duration is -1277910790 seconds.  Expecting to read -2555821580 L frames from the lopc.bin file.
INFO 2023-07-07 21:58:10,142 lopcToNetCDF.py constructTimestampList():1335 [55] recCount not passed in, assuming we'll have -2555821580 records from the lopc.bin file.
WARNING 2023-07-07 21:58:10,142 lopcToNetCDF.py main():2299 [55] No timestamp data found in file: /data/auv_data/dorado/missionlogs/2010.181.00/lopc.bin
INFO 2023-07-07 21:58:10,241 calibrate.py _nudge_pos():868 [55] seg#   end_sec_diff end_lon_diff end_lat_diff len(segi)   seg_min u_drift (cm/s) v_drift (cm/s)     start datetime of segment
INFO 2023-07-07 21:58:10,243 calibrate.py _nudge_pos():892 [55]                   -            -            -         0      0.00              -              -                             -
INFO 2023-07-07 21:58:18,653 calibrate.py _nudge_pos():987 [55]  1002:        0.130    0.0004507   -0.0006012      1765      5.88         11.358        -18.946 2010-06-30T15:35:46.536035328
INFO 2023-07-07 21:58:19,535 calibrate.py _nudge_pos():1044 [55] 1057:            -            -            -         0      0.00              -              -
INFO 2023-07-07 21:58:19,535 calibrate.py _nudge_pos():1050 [55] Points in final series = 7037
WARNING 2023-07-07 21:58:19,553 calibrate.py _depth_process():1289 [55] Expected sample_rate to be 10 Hz, instead it's 8.333333333333334 Hz
INFO 2023-07-07 21:58:20,842 calibrate.py _geometric_depth_correction():2333 [55] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 1433 seconds,
INFO 2023-07-07 21:58:20,961 calibrate.py _geometric_depth_correction():2333 [55] ctd1: d_beg_time_diff: 37 seconds, d_end_time_diff: 1432 seconds,
INFO 2023-07-07 21:58:20,963 calibrate.py _ctd_process():1934 [55] Performing range checking of ['ctd1_salinity'] in 2010.181.00/ctd1.nc
WARNING 2023-07-07 21:58:20,965 calibrate.py _range_qc_combined_nc():392 [55] More than 500 (2668) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data.
INFO 2023-07-07 21:58:20,965 calibrate.py _range_qc_combined_nc():400 [55] Setting 2668 ctd1_salinity values to NaN
INFO 2023-07-07 21:58:20,965 calibrate.py _range_qc_combined_nc():414 [55] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))]
INFO 2023-07-07 21:58:20,965 calibrate.py _range_qc_combined_nc():440 [55] Done range checking ctd1
INFO 2023-07-07 21:58:21,111 calibrate.py _geometric_depth_correction():2333 [55] ctd2: d_beg_time_diff: 37 seconds, d_end_time_diff: 1433 seconds,
INFO 2023-07-07 21:58:21,113 calibrate.py _ctd_process():1934 [55] Performing range checking of ['ctd2_salinity'] in 2010.181.00/ctd2.nc
WARNING 2023-07-07 21:58:21,115 calibrate.py _range_qc_combined_nc():392 [55] More than 500 (2658) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data.
INFO 2023-07-07 21:58:21,115 calibrate.py _range_qc_combined_nc():400 [55] Setting 2658 ctd2_salinity values to NaN
INFO 2023-07-07 21:58:21,115 calibrate.py _range_qc_combined_nc():414 [55] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))]
INFO 2023-07-07 21:58:21,115 calibrate.py _range_qc_combined_nc():440 [55] Done range checking ctd2
ERROR 2023-07-07 21:58:21,175 calibrate.py process_logs():2445 [55] Error processing biolume: biolume has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.181.00
ERROR 2023-07-07 21:58:21,175 calibrate.py process_logs():2445 [55] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.181.00
ERROR 2023-07-07 21:58:21,175 calibrate.py process_logs():2445 [55] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.181.00
INFO 2023-07-07 21:58:21,257 calibrate.py write_netcdf():2416 [55] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_cal.nc
INFO 2023-07-07 21:58:21,340 calibrate.py write_netcdf():2420 [55] Data variables written: ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bb420, hs2_bb700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time
INFO 2023-07-07 21:58:21,384 align.py process_cal():148 [55] Processing dorado_2010.181.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.181.00
INFO 2023-07-07 21:58:21,389 align.py process_cal():214 [55] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2023-07-07 21:58:21,390 align.py process_cal():267 [55] navigation_roll: Extrapolating 7038 value(s) at indices [   0    1    2 ... 7035 7036 7037]
ERROR 2023-07-07 21:58:21,390 align.py process_cal():277 [55] navigation_roll: Too many values would be extrapolated in call to interp1d() for variable navigation_roll
INFO 2023-07-07 21:58:21,390 align.py process_cal():280 [55] navigation_roll: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,395 align.py process_cal():214 [55] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2023-07-07 21:58:21,396 align.py process_cal():267 [55] navigation_pitch: Extrapolating 7038 value(s) at indices [   0    1    2 ... 7035 7036 7037]
ERROR 2023-07-07 21:58:21,396 align.py process_cal():277 [55] navigation_pitch: Too many values would be extrapolated in call to interp1d() for variable navigation_pitch
INFO 2023-07-07 21:58:21,396 align.py process_cal():280 [55] navigation_pitch: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,400 align.py process_cal():214 [55] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2023-07-07 21:58:21,402 align.py process_cal():267 [55] navigation_yaw: Extrapolating 7038 value(s) at indices [   0    1    2 ... 7035 7036 7037]
ERROR 2023-07-07 21:58:21,402 align.py process_cal():277 [55] navigation_yaw: Too many values would be extrapolated in call to interp1d() for variable navigation_yaw
INFO 2023-07-07 21:58:21,402 align.py process_cal():280 [55] navigation_yaw: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,402 align.py process_cal():171 [55] Skipping navigation_posx
INFO 2023-07-07 21:58:21,402 align.py process_cal():171 [55] Skipping navigation_posy
INFO 2023-07-07 21:58:21,406 align.py process_cal():214 [55] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2023-07-07 21:58:21,407 align.py process_cal():267 [55] navigation_mWaterSpeed: Extrapolating 7038 value(s) at indices [   0    1    2 ... 7035 7036 7037]
ERROR 2023-07-07 21:58:21,408 align.py process_cal():277 [55] navigation_mWaterSpeed: Too many values would be extrapolated in call to interp1d() for variable navigation_mWaterSpeed
INFO 2023-07-07 21:58:21,408 align.py process_cal():280 [55] navigation_mWaterSpeed: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,412 align.py process_cal():214 [55] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,413 align.py process_cal():267 [55] hs2_bb420: Extrapolating 5779 value(s) at indices [   0    1    2 ... 5776 5777 5778]
ERROR 2023-07-07 21:58:21,413 align.py process_cal():277 [55] hs2_bb420: Too many values would be extrapolated in call to interp1d() for variable hs2_bb420
INFO 2023-07-07 21:58:21,413 align.py process_cal():280 [55] hs2_bb420: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,418 align.py process_cal():214 [55] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,419 align.py process_cal():267 [55] hs2_bb700: Extrapolating 5779 value(s) at indices [   0    1    2 ... 5776 5777 5778]
ERROR 2023-07-07 21:58:21,419 align.py process_cal():277 [55] hs2_bb700: Too many values would be extrapolated in call to interp1d() for variable hs2_bb700
INFO 2023-07-07 21:58:21,419 align.py process_cal():280 [55] hs2_bb700: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,423 align.py process_cal():214 [55] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,424 align.py process_cal():267 [55] hs2_fl700: Extrapolating 5779 value(s) at indices [   0    1    2 ... 5776 5777 5778]
ERROR 2023-07-07 21:58:21,425 align.py process_cal():277 [55] hs2_fl700: Too many values would be extrapolated in call to interp1d() for variable hs2_fl700
INFO 2023-07-07 21:58:21,425 align.py process_cal():280 [55] hs2_fl700: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,429 align.py process_cal():214 [55] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,430 align.py process_cal():267 [55] hs2_depth: Extrapolating 5779 value(s) at indices [   0    1    2 ... 5776 5777 5778]
ERROR 2023-07-07 21:58:21,430 align.py process_cal():277 [55] hs2_depth: Too many values would be extrapolated in call to interp1d() for variable hs2_depth
INFO 2023-07-07 21:58:21,430 align.py process_cal():280 [55] hs2_depth: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,435 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,436 align.py process_cal():267 [55] ctd1_temperature: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,436 align.py process_cal():277 [55] ctd1_temperature: Too many values would be extrapolated in call to interp1d() for variable ctd1_temperature
INFO 2023-07-07 21:58:21,436 align.py process_cal():280 [55] ctd1_temperature: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,441 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,442 align.py process_cal():267 [55] ctd1_conductivity: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,442 align.py process_cal():277 [55] ctd1_conductivity: Too many values would be extrapolated in call to interp1d() for variable ctd1_conductivity
INFO 2023-07-07 21:58:21,442 align.py process_cal():280 [55] ctd1_conductivity: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,447 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,448 align.py process_cal():267 [55] ctd1_salinity: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,448 align.py process_cal():277 [55] ctd1_salinity: Too many values would be extrapolated in call to interp1d() for variable ctd1_salinity
INFO 2023-07-07 21:58:21,448 align.py process_cal():280 [55] ctd1_salinity: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,453 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,454 align.py process_cal():267 [55] ctd1_temperature_onboard: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,454 align.py process_cal():277 [55] ctd1_temperature_onboard: Too many values would be extrapolated in call to interp1d() for variable ctd1_temperature_onboard
INFO 2023-07-07 21:58:21,454 align.py process_cal():280 [55] ctd1_temperature_onboard: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,459 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,460 align.py process_cal():267 [55] ctd1_conductivity_onboard: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,460 align.py process_cal():277 [55] ctd1_conductivity_onboard: Too many values would be extrapolated in call to interp1d() for variable ctd1_conductivity_onboard
INFO 2023-07-07 21:58:21,460 align.py process_cal():280 [55] ctd1_conductivity_onboard: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,465 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,466 align.py process_cal():267 [55] ctd1_salinity_onboard: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,466 align.py process_cal():277 [55] ctd1_salinity_onboard: Too many values would be extrapolated in call to interp1d() for variable ctd1_salinity_onboard
INFO 2023-07-07 21:58:21,466 align.py process_cal():280 [55] ctd1_salinity_onboard: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,471 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,472 align.py process_cal():267 [55] ctd1_dissolvedO2: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,472 align.py process_cal():277 [55] ctd1_dissolvedO2: Too many values would be extrapolated in call to interp1d() for variable ctd1_dissolvedO2
INFO 2023-07-07 21:58:21,472 align.py process_cal():280 [55] ctd1_dissolvedO2: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,477 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,478 align.py process_cal():267 [55] ctd1_oxygen_mll: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,478 align.py process_cal():277 [55] ctd1_oxygen_mll: Too many values would be extrapolated in call to interp1d() for variable ctd1_oxygen_mll
INFO 2023-07-07 21:58:21,478 align.py process_cal():280 [55] ctd1_oxygen_mll: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,483 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,484 align.py process_cal():267 [55] ctd1_oxygen_umolkg: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,484 align.py process_cal():277 [55] ctd1_oxygen_umolkg: Too many values would be extrapolated in call to interp1d() for variable ctd1_oxygen_umolkg
INFO 2023-07-07 21:58:21,484 align.py process_cal():280 [55] ctd1_oxygen_umolkg: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,489 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,490 align.py process_cal():267 [55] ctd1_flow1: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,490 align.py process_cal():277 [55] ctd1_flow1: Too many values would be extrapolated in call to interp1d() for variable ctd1_flow1
INFO 2023-07-07 21:58:21,491 align.py process_cal():280 [55] ctd1_flow1: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,495 align.py process_cal():214 [55] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,497 align.py process_cal():267 [55] ctd1_depth: Extrapolating 5660 value(s) at indices [   0    1    2 ... 5657 5658 5659]
ERROR 2023-07-07 21:58:21,497 align.py process_cal():277 [55] ctd1_depth: Too many values would be extrapolated in call to interp1d() for variable ctd1_depth
INFO 2023-07-07 21:58:21,497 align.py process_cal():280 [55] ctd1_depth: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,502 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,503 align.py process_cal():267 [55] ctd2_temperature: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,503 align.py process_cal():277 [55] ctd2_temperature: Too many values would be extrapolated in call to interp1d() for variable ctd2_temperature
INFO 2023-07-07 21:58:21,504 align.py process_cal():280 [55] ctd2_temperature: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,509 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,510 align.py process_cal():267 [55] ctd2_conductivity: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,510 align.py process_cal():277 [55] ctd2_conductivity: Too many values would be extrapolated in call to interp1d() for variable ctd2_conductivity
INFO 2023-07-07 21:58:21,510 align.py process_cal():280 [55] ctd2_conductivity: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,515 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,516 align.py process_cal():267 [55] ctd2_salinity: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,517 align.py process_cal():277 [55] ctd2_salinity: Too many values would be extrapolated in call to interp1d() for variable ctd2_salinity
INFO 2023-07-07 21:58:21,517 align.py process_cal():280 [55] ctd2_salinity: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,522 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,523 align.py process_cal():267 [55] ctd2_temperature_onboard: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,523 align.py process_cal():277 [55] ctd2_temperature_onboard: Too many values would be extrapolated in call to interp1d() for variable ctd2_temperature_onboard
INFO 2023-07-07 21:58:21,523 align.py process_cal():280 [55] ctd2_temperature_onboard: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,529 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,530 align.py process_cal():267 [55] ctd2_conductivity_onboard: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,530 align.py process_cal():277 [55] ctd2_conductivity_onboard: Too many values would be extrapolated in call to interp1d() for variable ctd2_conductivity_onboard
INFO 2023-07-07 21:58:21,530 align.py process_cal():280 [55] ctd2_conductivity_onboard: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,535 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,537 align.py process_cal():267 [55] ctd2_salinity_onboard: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,537 align.py process_cal():277 [55] ctd2_salinity_onboard: Too many values would be extrapolated in call to interp1d() for variable ctd2_salinity_onboard
INFO 2023-07-07 21:58:21,537 align.py process_cal():280 [55] ctd2_salinity_onboard: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,542 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,543 align.py process_cal():267 [55] ctd2_flow2: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,544 align.py process_cal():277 [55] ctd2_flow2: Too many values would be extrapolated in call to interp1d() for variable ctd2_flow2
INFO 2023-07-07 21:58:21,544 align.py process_cal():280 [55] ctd2_flow2: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,549 align.py process_cal():214 [55] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.181.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0)
INFO 2023-07-07 21:58:21,550 align.py process_cal():267 [55] ctd2_depth: Extrapolating 5661 value(s) at indices [   0    1    2 ... 5658 5659 5660]
ERROR 2023-07-07 21:58:21,550 align.py process_cal():277 [55] ctd2_depth: Too many values would be extrapolated in call to interp1d() for variable ctd2_depth
INFO 2023-07-07 21:58:21,550 align.py process_cal():280 [55] ctd2_depth: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,556 align.py process_cal():267 [55] isus_nitrate: Extrapolating 1093 value(s) at indices [   0    1    2 ... 1090 1091 1092]
ERROR 2023-07-07 21:58:21,557 align.py process_cal():277 [55] isus_nitrate: Too many values would be extrapolated in call to interp1d() for variable isus_nitrate
INFO 2023-07-07 21:58:21,557 align.py process_cal():280 [55] isus_nitrate: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,562 align.py process_cal():267 [55] isus_temp: Extrapolating 1093 value(s) at indices [   0    1    2 ... 1090 1091 1092]
ERROR 2023-07-07 21:58:21,562 align.py process_cal():277 [55] isus_temp: Too many values would be extrapolated in call to interp1d() for variable isus_temp
INFO 2023-07-07 21:58:21,563 align.py process_cal():280 [55] isus_temp: Too many values would be extrapolated, not saving it in _align.nc
INFO 2023-07-07 21:58:21,569 align.py process_cal():267 [55] tailcone_propRpm: Extrapolating 7216 value(s) at indices [   0    1    2 ... 7213 7214 7215]
ERROR 2023-07-07 21:58:21,569 align.py process_cal():277 [55] tailcone_propRpm: Too many values would be extrapolated in call to interp1d() for variable tailcone_propRpm
INFO 2023-07-07 21:58:21,569 align.py process_cal():280 [55] tailcone_propRpm: Too many values would be extrapolated, not saving it in _align.nc
WARNING 2023-07-07 21:58:21,574 align.py global_metadata():64 [55] could not get head commit sha for git@github.com:mbari-org/auv-python.git: SHA could not be resolved, git returned: b''
WARNING 2023-07-07 21:58:21,574 align.py global_metadata():87 [55] Could not save time_coverage_duration - likely because all data are bad and min_time and max_time were not set
INFO 2023-07-07 21:58:21,574 align.py write_netcdf():406 [55] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_align.nc
INFO 2023-07-07 21:58:21,632 align.py write_netcdf():411 [55] Data variables written: ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bb420, hs2_bb700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_propRpm, tailcone_time
INFO 2023-07-07 21:58:21,665 resample.py instruments_variables():232 [55] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_align.nc mission netCDF file
INFO 2023-07-07 21:58:21,671 resample.py instruments_variables():232 [55] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_align.nc mission netCDF file
INFO 2023-07-07 21:58:21,672 resample.py get_mission_start_end():806 [55] navigation: 2010-06-30T15:14:01.115462656 to 2010-06-30T15:37:28.539047424 (0 days 00:00:00.109992448 before mission_end)
INFO 2023-07-07 21:58:21,674 resample.py get_mission_start_end():806 [55] hs2       : 2010-06-30T15:13:23.028071936 to 2010-06-30T15:37:28.649039872 (0 days 00:00:00 before mission_end)
INFO 2023-07-07 21:58:21,675 resample.py get_mission_start_end():806 [55] ctd1      : 2010-06-30T15:13:53.765966080 to 2010-06-30T15:37:28.479051520 (0 days 00:00:00.169988352 before mission_end)
INFO 2023-07-07 21:58:21,676 resample.py get_mission_start_end():806 [55] ctd2      : 2010-06-30T15:13:53.545981184 to 2010-06-30T15:37:28.509049600 (0 days 00:00:00.139990272 before mission_end)
INFO 2023-07-07 21:58:21,678 resample.py get_mission_start_end():806 [55] isus      : 2010-06-30T15:14:13.484615424 to 2010-06-30T15:37:28.579044864 (0 days 00:00:00.069995008 before mission_end)
INFO 2023-07-07 21:58:21,679 resample.py get_mission_start_end():806 [55] tailcone  : 2010-06-30T15:13:14.838632704 to 2010-06-30T15:37:28.639040768 (0 days 00:00:00.009999104 before mission_end)
INFO 2023-07-07 21:58:21,680 resample.py instruments_variables():232 [55] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_align.nc mission netCDF file
INFO 2023-07-07 21:58:21,681 resample.py resample_coordinates():246 [55] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter 
WARNING 2023-07-07 21:58:21,682 resample.py resample_coordinates():268 [55] Variable ctd1_latitude or ctd1_longitude not found in 2010.181.00 align.nc file
ERROR 2023-07-07 21:58:21,682 process.py process_mission_job():341 [55] 2010.181.00 Variable ctd1_latitude or ctd1_longitude not found in 2010.181.00 align.nc file
ERROR 2023-07-07 21:58:21,682 process.py process_mission_job():342 [55] Cannot continue without valid file(s)
INFO 2023-07-07 21:58:21,684 archive.py copy_to_AUVTCD():45 [55] Copying /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00 files to /Volumes/AUVCTD/surveys/2010/netcdf
ERROR 2023-07-07 21:58:21,685 archive.py copy_to_AUVTCD():54 [55] /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_1S.nc not found
INFO 2023-07-07 21:58:21,758 archive.py copy_to_AUVTCD():52 [55] rsync /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done.
INFO 2023-07-07 21:58:21,817 archive.py copy_to_AUVTCD():52 [55] rsync /data/auv_data/dorado/missionnetcdfs/2010.181.00/dorado_2010.181.00_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done.