INFO 2025-06-26 10:44:04,789 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber
INFO 2025-06-26 10:44:04,789 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Portaled 7/26/05 - ctdToUse = ctd1 
INFO 2025-06-26 10:44:04,789 process.py process_mission():449 [1] Processing BIOLUME mission 2005.203.01 by user docker_user on host eae60d30a712
INFO 2025-06-26 10:44:04,789 process.py download_process():165 [1] Download and processing steps for 2005.203.01
INFO 2025-06-26 10:44:04,789 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2005/2005203/2005.203.01
INFO 2025-06-26 10:44:04,790 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2005/2005203/2005.203.01 to /data/auv_data/dorado/missionlogs/2005.203.01
INFO 2025-06-26 10:44:04,895 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2005.203.01
INFO 2025-06-26 10:44:04,895 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/ctdDriver.log (256651 bytes)
INFO 2025-06-26 10:44:04,922 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/ctdDriver2.log (256469 bytes)
INFO 2025-06-26 10:44:04,947 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/gps.log (17996 bytes)
INFO 2025-06-26 10:44:04,956 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/hydroscatlog.log (180974 bytes)
INFO 2025-06-26 10:44:04,984 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/navigation.log (866304 bytes)
WARNING 2025-06-26 10:44:05,030 logs2netcdfs.py _read_data():216 [1] unpack requires a buffer of 8 bytes, b = b'\xd8j0I\xd6$' at record 3662, for mPhi in file /data/auv_data/dorado/missionlogs/2005.203.01/navigation.log
INFO 2025-06-26 10:44:05,030 logs2netcdfs.py _read_data():224 [1] bytes read = 866306 file size = 866304
INFO 2025-06-26 10:44:05,030 logs2netcdfs.py _read_data():229 [1] Tried to read 8 bytes, but only 2 bytes remaining
INFO 2025-06-26 10:44:05,030 logs2netcdfs.py _read_data():235 [1] Successfully unpacked 3662 records
WARNING 2025-06-26 10:44:05,037 logs2netcdfs.py _create_variable():536 [1] mTheta: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,037 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mTheta.shape[0] (3663)
WARNING 2025-06-26 10:44:05,037 logs2netcdfs.py _create_variable():544 [1] mTheta data is short by one, appending the last value: -0.012080098699101639
WARNING 2025-06-26 10:44:05,038 logs2netcdfs.py _create_variable():536 [1] mPsi: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,038 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mPsi.shape[0] (3663)
WARNING 2025-06-26 10:44:05,038 logs2netcdfs.py _create_variable():544 [1] mPsi data is short by one, appending the last value: 5.223978817545509
WARNING 2025-06-26 10:44:05,039 logs2netcdfs.py _create_variable():536 [1] mOmega_x: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,039 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mOmega_x.shape[0] (3663)
WARNING 2025-06-26 10:44:05,039 logs2netcdfs.py _create_variable():544 [1] mOmega_x data is short by one, appending the last value: 0.15140070801234723
WARNING 2025-06-26 10:44:05,040 logs2netcdfs.py _create_variable():536 [1] mOmega_y: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,040 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mOmega_y.shape[0] (3663)
WARNING 2025-06-26 10:44:05,040 logs2netcdfs.py _create_variable():544 [1] mOmega_y data is short by one, appending the last value: 0.0756604065898115
WARNING 2025-06-26 10:44:05,041 logs2netcdfs.py _create_variable():536 [1] mOmega_z: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,041 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mOmega_z.shape[0] (3663)
WARNING 2025-06-26 10:44:05,042 logs2netcdfs.py _create_variable():544 [1] mOmega_z data is short by one, appending the last value: -0.07230482361539536
WARNING 2025-06-26 10:44:05,042 logs2netcdfs.py _create_variable():536 [1] mPsaRange: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,043 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mPsaRange.shape[0] (3663)
WARNING 2025-06-26 10:44:05,043 logs2netcdfs.py _create_variable():544 [1] mPsaRange data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,044 logs2netcdfs.py _create_variable():536 [1] mAltitude: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,044 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mAltitude.shape[0] (3663)
WARNING 2025-06-26 10:44:05,044 logs2netcdfs.py _create_variable():544 [1] mAltitude data is short by one, appending the last value: 17.26745456108638
WARNING 2025-06-26 10:44:05,045 logs2netcdfs.py _create_variable():536 [1] mDvlAltitude: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,045 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mDvlAltitude.shape[0] (3663)
WARNING 2025-06-26 10:44:05,045 logs2netcdfs.py _create_variable():544 [1] mDvlAltitude data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,046 logs2netcdfs.py _create_variable():536 [1] mWaterSpeed: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,046 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mWaterSpeed.shape[0] (3663)
WARNING 2025-06-26 10:44:05,046 logs2netcdfs.py _create_variable():544 [1] mWaterSpeed data is short by one, appending the last value: 0.277
WARNING 2025-06-26 10:44:05,047 logs2netcdfs.py _create_variable():536 [1] mDvlValid: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,047 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mDvlValid.shape[0] (3663)
WARNING 2025-06-26 10:44:05,047 logs2netcdfs.py _create_variable():544 [1] mDvlValid data is short by one, appending the last value: 1
WARNING 2025-06-26 10:44:05,048 logs2netcdfs.py _create_variable():536 [1] mDvlNewData: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,048 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mDvlNewData.shape[0] (3663)
WARNING 2025-06-26 10:44:05,048 logs2netcdfs.py _create_variable():544 [1] mDvlNewData data is short by one, appending the last value: 1
WARNING 2025-06-26 10:44:05,049 logs2netcdfs.py _create_variable():536 [1] mDeltaT: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,049 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of mDeltaT.shape[0] (3663)
WARNING 2025-06-26 10:44:05,050 logs2netcdfs.py _create_variable():544 [1] mDeltaT data is short by one, appending the last value: 0.7999451160430908
WARNING 2025-06-26 10:44:05,050 logs2netcdfs.py _create_variable():536 [1] nfix: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,051 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of nfix.shape[0] (3663)
WARNING 2025-06-26 10:44:05,051 logs2netcdfs.py _create_variable():544 [1] nfix data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,052 logs2netcdfs.py _create_variable():536 [1] efix: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,052 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of efix.shape[0] (3663)
WARNING 2025-06-26 10:44:05,052 logs2netcdfs.py _create_variable():544 [1] efix data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,053 logs2netcdfs.py _create_variable():536 [1] filter_north: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,053 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of filter_north.shape[0] (3663)
WARNING 2025-06-26 10:44:05,053 logs2netcdfs.py _create_variable():544 [1] filter_north data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,054 logs2netcdfs.py _create_variable():536 [1] filter_east: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,054 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of filter_east.shape[0] (3663)
WARNING 2025-06-26 10:44:05,054 logs2netcdfs.py _create_variable():544 [1] filter_east data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,055 logs2netcdfs.py _create_variable():536 [1] filter_depth: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,055 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of filter_depth.shape[0] (3663)
WARNING 2025-06-26 10:44:05,055 logs2netcdfs.py _create_variable():544 [1] filter_depth data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,056 logs2netcdfs.py _create_variable():536 [1] north_current: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,056 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of north_current.shape[0] (3663)
WARNING 2025-06-26 10:44:05,056 logs2netcdfs.py _create_variable():544 [1] north_current data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,057 logs2netcdfs.py _create_variable():536 [1] east_current: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,057 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of east_current.shape[0] (3663)
WARNING 2025-06-26 10:44:05,057 logs2netcdfs.py _create_variable():544 [1] east_current data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,058 logs2netcdfs.py _create_variable():536 [1] speed_bias: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,059 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of speed_bias.shape[0] (3663)
WARNING 2025-06-26 10:44:05,059 logs2netcdfs.py _create_variable():544 [1] speed_bias data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,060 logs2netcdfs.py _create_variable():536 [1] heading_bias: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,060 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of heading_bias.shape[0] (3663)
WARNING 2025-06-26 10:44:05,060 logs2netcdfs.py _create_variable():544 [1] heading_bias data is short by one, appending the last value: 0.0
WARNING 2025-06-26 10:44:05,061 logs2netcdfs.py _create_variable():536 [1] latitude: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,061 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of latitude.shape[0] (3663)
WARNING 2025-06-26 10:44:05,061 logs2netcdfs.py _create_variable():544 [1] latitude data is short by one, appending the last value: 0.6444953221096232
WARNING 2025-06-26 10:44:05,062 logs2netcdfs.py _create_variable():536 [1] longitude: shape mismatch: objects cannot be broadcast to a single shape.  Mismatch is between arg 0 with shape (3663,) and arg 1 with shape (3662,).
INFO 2025-06-26 10:44:05,062 logs2netcdfs.py _create_variable():537 [1] len(data) (3662) does not match shape of longitude.shape[0] (3663)
WARNING 2025-06-26 10:44:05,062 logs2netcdfs.py _create_variable():544 [1] longitude data is short by one, appending the last value: -2.1275692084533784
INFO 2025-06-26 10:44:05,074 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/isuslog.log (14549 bytes)
INFO 2025-06-26 10:44:05,080 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/parosci.log (387494 bytes)
INFO 2025-06-26 10:44:05,117 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/tailCone.log (181723 bytes)
INFO 2025-06-26 10:44:05,146 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2005.203.01/biolume.log (208220 bytes)
INFO 2025-06-26 10:44:05,169 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data
INFO 2025-06-26 10:44:05,182 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.29 seconds
WARNING 2025-06-26 10:44:05,183 process.py download_process():196 [1] No lopc.bin file for 2005.203.01
INFO 2025-06-26 10:44:05,183 process.py calibrate():227 [1] Calibration steps for 2005.203.01
INFO 2025-06-26 10:44:05,242 calibrate.py _nudge_pos():1680 [1] 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 2025-06-26 10:44:05,243 calibrate.py _nudge_pos():1711 [1]                   -            -            -         0      0.00              -              -                             -
INFO 2025-06-26 10:44:06,977 calibrate.py _nudge_pos():1806 [1]   203:        0.110   -0.0005494   -0.0028459      2595      8.65         -9.412        -60.989 2005-07-22T04:19:06.683831424
INFO 2025-06-26 10:44:07,296 calibrate.py _nudge_pos():1862 [1]  216:            -            -            -         0      0.00              -              -
INFO 2025-06-26 10:44:07,296 calibrate.py _nudge_pos():1868 [1] Points in final series = 3663
WARNING 2025-06-26 10:44:07,306 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz
INFO 2025-06-26 10:44:07,349 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds
INFO 2025-06-26 10:44:07,397 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds
INFO 2025-06-26 10:44:07,421 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds
INFO 2025-06-26 10:44:07,422 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2005.203.01/ctd1.nc
INFO 2025-06-26 10:44:07,423 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN
INFO 2025-06-26 10:44:07,423 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))]
INFO 2025-06-26 10:44:07,423 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1
INFO 2025-06-26 10:44:07,463 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds
INFO 2025-06-26 10:44:07,488 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds
INFO 2025-06-26 10:44:07,489 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2005.203.01/ctd2.nc
INFO 2025-06-26 10:44:07,490 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN
INFO 2025-06-26 10:44:07,491 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))]
INFO 2025-06-26 10:44:07,491 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2
INFO 2025-06-26 10:44:07,498 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz
INFO 2025-06-26 10:44:07,530 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60]
INFO 2025-06-26 10:44:07,539 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds
ERROR 2025-06-26 10:44:07,543 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']"
ERROR 2025-06-26 10:44:07,544 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.203.01
ERROR 2025-06-26 10:44:07,544 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2005.203.01
INFO 2025-06-26 10:44:07,550 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_cal.nc
INFO 2025-06-26 10:44:07,591 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, 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 2025-06-26 10:44:07,595 process.py align():251 [1] Alignment steps for 2005.203.01
INFO 2025-06-26 10:44:07,615 align.py process_cal():139 [1] Processing dorado_2005.203.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2005.203.01
INFO 2025-06-26 10:44:07,620 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 10:44:07,622 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 10:44:07,633 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 10:44:07,635 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 10:44:07,645 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 10:44:07,646 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 10:44:07,652 align.py process_cal():161 [1] Skipping navigation_posx
INFO 2025-06-26 10:44:07,652 align.py process_cal():161 [1] Skipping navigation_posy
INFO 2025-06-26 10:44:07,656 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc
INFO 2025-06-26 10:44:07,658 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 10:44:07,667 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794)
INFO 2025-06-26 10:44:07,669 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,680 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794)
INFO 2025-06-26 10:44:07,681 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,691 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794)
INFO 2025-06-26 10:44:07,693 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,703 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,705 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,715 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,716 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,726 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,728 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,738 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,740 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,750 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,752 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,762 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,764 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,774 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,775 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,786 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,787 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,798 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,799 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,810 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,812 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,822 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,824 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,835 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,837 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,847 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,849 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,860 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,861 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,872 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,874 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,884 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,886 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,897 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2005.203.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001)
INFO 2025-06-26 10:44:07,899 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00
INFO 2025-06-26 10:44:07,912 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.67
INFO 2025-06-26 10:44:07,925 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.67
INFO 2025-06-26 10:44:07,938 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.67
INFO 2025-06-26 10:44:07,952 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00
INFO 2025-06-26 10:44:07,966 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00
INFO 2025-06-26 10:44:07,978 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_align.nc
INFO 2025-06-26 10:44:08,020 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time
INFO 2025-06-26 10:44:08,022 process.py resample():273 [1] Resampling steps for 2005.203.01
INFO 2025-06-26 10:44:08,023 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m
INFO 2025-06-26 10:44:08,043 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_align.nc mission netCDF file
INFO 2025-06-26 10:44:08,047 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_align.nc mission netCDF file
INFO 2025-06-26 10:44:08,048 resample.py get_mission_start_end():1145 [1] navigation: 2005-07-22T04:07:28.111686912 to 2005-07-22T04:19:40.491515392 (0 days 00:00:00.299979392 before mission_end)
INFO 2025-06-26 10:44:08,049 resample.py get_mission_start_end():1145 [1] hs2       : 2005-07-22T04:07:10.272908928 to 2005-07-22T04:19:40.781495552 (0 days 00:00:00.009999232 before mission_end)
INFO 2025-06-26 10:44:08,051 resample.py get_mission_start_end():1145 [1] ctd1      : 2005-07-22T04:07:33.651307392 to 2005-07-22T04:19:40.631505920 (0 days 00:00:00.159988864 before mission_end)
INFO 2025-06-26 10:44:08,052 resample.py get_mission_start_end():1145 [1] ctd2      : 2005-07-22T04:07:34.161272576 to 2005-07-22T04:19:40.631505920 (0 days 00:00:00.159988864 before mission_end)
INFO 2025-06-26 10:44:08,053 resample.py get_mission_start_end():1145 [1] isus      : 2005-07-22T04:08:36.956970752 to 2005-07-22T04:19:39.741566848 (0 days 00:00:01.049927936 before mission_end)
INFO 2025-06-26 10:44:08,054 resample.py get_mission_start_end():1145 [1] biolume   : 2005-07-22T04:07:05.503201536 to 2005-07-22T04:19:39.401555840 (0 days 00:00:01.389938944 before mission_end)
INFO 2025-06-26 10:44:08,056 resample.py get_mission_start_end():1145 [1] tailcone  : 2005-07-22T04:07:05.793215744 to 2005-07-22T04:19:40.791494784 (0 days 00:00:00 before mission_end)
INFO 2025-06-26 10:44:08,056 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_align.nc mission netCDF file
INFO 2025-06-26 10:44:08,057 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter 
INFO 2025-06-26 10:44:08,091 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,100 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,109 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,117 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,127 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,135 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,144 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,152 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,160 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,168 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,175 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,182 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,190 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,197 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,205 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,212 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,221 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,230 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,239 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,247 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,256 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,264 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,273 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,281 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,289 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,298 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,308 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter
INFO 2025-06-26 10:44:08,403 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_1S.nc
INFO 2025-06-26 10:44:08,904 create_products.py gulper_odv():401 [1] No gulper times found for 2005.203.01
INFO 2025-06-26 10:44:08,904 process.py archive():337 [1] Archiving steps for 2005.203.01
INFO 2025-06-26 10:44:08,904 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01, BASE_PATH = /data/auv_data
INFO 2025-06-26 10:44:08,904 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01 files to /Volumes/AUVCTD/surveys/2005/netcdf
INFO 2025-06-26 10:44:08,905 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.203.01_1S.nc
INFO 2025-06-26 10:44:08,913 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_1S.nc /Volumes/AUVCTD/surveys/2005/netcdf done.
INFO 2025-06-26 10:44:08,914 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.203.01_cal.nc
INFO 2025-06-26 10:44:08,923 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_cal.nc /Volumes/AUVCTD/surveys/2005/netcdf done.
INFO 2025-06-26 10:44:08,924 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2005/netcdf/dorado_2005.203.01_align.nc
INFO 2025-06-26 10:44:08,934 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_align.nc /Volumes/AUVCTD/surveys/2005/netcdf done.
INFO 2025-06-26 10:44:08,941 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,947 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,952 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,957 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,965 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,969 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,976 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,981 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,988 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2005/2005203/2005.203.01 done.
INFO 2025-06-26 10:44:08,989 archive.py copy_to_AUVTCD():116 [1] Archiving product files
INFO 2025-06-26 10:44:08,989 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2005.203.01/dorado_2005.203.01_processing.log /Volumes/AUVCTD/surveys/2005/netcdf