INFO 2025-06-26 15:02:28,427 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 15:02:28,427 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Ryan - around ESP - ctdToUse = ctd2 INFO 2025-06-26 15:02:28,427 process.py process_mission():449 [1] Processing AUVCTD mission 2009.155.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:02:28,427 process.py download_process():165 [1] Download and processing steps for 2009.155.03 INFO 2025-06-26 15:02:28,427 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009155/2009.155.03 INFO 2025-06-26 15:02:28,427 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009155/2009.155.03 to /data/auv_data/dorado/missionlogs/2009.155.03 INFO 2025-06-26 15:02:31,643 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.155.03 INFO 2025-06-26 15:02:31,643 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/ctdDriver.log (3317646 bytes) INFO 2025-06-26 15:02:31,894 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/ctdDriver2.log (3317637 bytes) INFO 2025-06-26 15:02:32,180 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/gps.log (407588 bytes) INFO 2025-06-26 15:02:32,231 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/hydroscatlog.log (3170350 bytes) INFO 2025-06-26 15:02:32,563 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/navigation.log (11104398 bytes) INFO 2025-06-26 15:02:33,396 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/isuslog.log (220021 bytes) INFO 2025-06-26 15:02:33,422 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/parosci.log (3865814 bytes) INFO 2025-06-26 15:02:33,790 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/tailCone.log (523243 bytes) INFO 2025-06-26 15:02:33,873 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/biolume.log (2571356 bytes) INFO 2025-06-26 15:02:34,146 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 15:02:34,316 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.67 seconds INFO 2025-06-26 15:02:34,316 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.155.03/lopc.bin (21405749 bytes) INFO 2025-06-26 15:02:34,316 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:02:34 2025 INFO 2025-06-26 15:02:34,317 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.155.03/parosci.nc INFO 2025-06-26 15:02:34,317 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:02:34,317 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.155.03/parosci.nc INFO 2025-06-26 15:02:34,321 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1244138913.7, sensor_off_time = 1244148355.5 INFO 2025-06-26 15:02:34,321 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 9441 seconds. Expecting to read 18882 L frames from the lopc.bin file. INFO 2025-06-26 15:02:34,322 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 18882 records from the lopc.bin file. INFO 2025-06-26 15:02:34,436 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-06-04 18:08:33 Z and endTime = 2009-06-04 20:45:55 Z with 18882 records expected to be read from lopc.bin INFO 2025-06-26 15:02:34,437 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.155.03/lopc.bin INFO 2025-06-26 15:02:34,437 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.155.03/lopc.nc INFO 2025-06-26 15:02:34,437 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.155.03/lopc.nc INFO 2025-06-26 15:02:34,438 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.155.03 INFO 2025-06-26 15:02:34,438 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:02:34,508 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:02:34,508 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:02:34,508 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 15:02:34,796 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 15:02:34,797 process.py calibrate():227 [1] Calibration steps for 2009.155.03 INFO 2025-06-26 15:02:34,943 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 15:02:34,945 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:02:36,114 calibrate.py _nudge_pos():1806 [1] 142: 0.020 0.0028849 -0.0012361 9110 30.36 14.088 -7.544 2009-06-04T18:41:16.641584384 INFO 2025-06-26 15:02:37,274 calibrate.py _nudge_pos():1806 [1] 265: 0.030 0.0010451 -0.0004173 3980 13.26 11.683 -5.830 2009-06-04T18:56:34.638697216 INFO 2025-06-26 15:02:37,324 calibrate.py _nudge_pos():1806 [1] 270: 0.020 0.0009041 -0.0005597 5470 18.23 7.351 -5.689 2009-06-04T19:14:52.643478528 INFO 2025-06-26 15:02:59,925 calibrate.py _nudge_pos():1806 [1] 2590: 0.020 0.0000123 0.0000078 75 0.25 7.393 5.834 2009-06-04T19:53:46.643588864 INFO 2025-06-26 15:03:19,265 calibrate.py _nudge_pos():1806 [1] 4589: 0.030 0.0000157 0.0000120 60 0.20 11.804 11.268 2009-06-04T20:27:16.635894784 INFO 2025-06-26 15:03:24,386 calibrate.py _nudge_pos():1806 [1] 5122: 0.040 -0.0002953 -0.0002432 300 1.00 -43.921 -45.210 2009-06-04T20:37:08.635340288 INFO 2025-06-26 15:03:29,439 calibrate.py _nudge_pos():1862 [1] 5616: - - - 4 0.01 - - INFO 2025-06-26 15:03:29,439 calibrate.py _nudge_pos():1868 [1] Points in final series = 47044 INFO 2025-06-26 15:03:29,502 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=50) for self.args.mission=2009.155.03 INFO 2025-06-26 15:03:29,505 calibrate.py _depth_process():2175 [1] Setting 8 depths values to NaN WARNING 2025-06-26 15:03:29,507 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:03:29,582 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1500 of 37730 INFO 2025-06-26 15:03:29,880 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:03:30,257 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:03:30,549 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:03:30,550 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.155.03/ctd1.nc WARNING 2025-06-26 15:03:30,552 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1845) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 15:03:30,552 calibrate.py _range_qc_combined_nc():898 [1] Setting 1845 ctd1_salinity values to NaN INFO 2025-06-26 15:03:30,552 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 15:03:30,552 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:03:30,902 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:03:31,217 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:03:31,219 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.155.03/ctd2.nc WARNING 2025-06-26 15:03:31,220 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1941) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 15:03:31,221 calibrate.py _range_qc_combined_nc():898 [1] Setting 1941 ctd2_salinity values to NaN INFO 2025-06-26 15:03:31,221 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 15:03:31,221 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:03:31,240 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:03:31,754 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 6540 6541 513960] INFO 2025-06-26 15:03:31,863 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:03:31,868 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 15:03:31,868 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2009.155.03 ERROR 2025-06-26 15:03:31,869 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.155.03 INFO 2025-06-26 15:03:31,883 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_cal.nc INFO 2025-06-26 15:03:31,956 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_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, 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 15:03:31,964 process.py align():251 [1] Alignment steps for 2009.155.03 INFO 2025-06-26 15:03:32,000 align.py process_cal():139 [1] Processing dorado_2009.155.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.155.03 INFO 2025-06-26 15:03:32,024 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:03:32,028 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:03:32,076 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:03:32,079 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:03:32,118 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:03:32,122 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:03:32,144 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:03:32,145 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:03:32,159 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:03:32,163 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:03:32,202 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,205 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 15:03:32,239 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,242 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 15:03:32,275 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,279 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 15:03:32,311 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,315 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,350 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,354 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,386 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,390 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,423 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,427 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,460 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,463 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,497 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,500 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,533 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,537 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,571 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,574 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,608 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,612 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,646 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,649 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,684 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,687 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,723 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,727 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,761 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,764 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,799 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,803 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,838 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,842 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,886 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,890 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,923 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.155.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:03:32,926 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:03:32,968 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:03:32,999 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:03:33,030 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:03:33,065 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:03:33,097 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.15 INFO 2025-06-26 15:03:33,112 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_align.nc INFO 2025-06-26 15:03:33,174 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_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, 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 15:03:33,177 process.py resample():273 [1] Resampling steps for 2009.155.03 INFO 2025-06-26 15:03:33,177 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:03:33,202 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_align.nc mission netCDF file INFO 2025-06-26 15:03:33,207 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_align.nc mission netCDF file INFO 2025-06-26 15:03:33,208 resample.py get_mission_start_end():1145 [1] navigation: 2009-06-04T18:09:06.853783808 to 2009-06-04T20:45:55.439251712 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 15:03:33,210 resample.py get_mission_start_end():1145 [1] hs2 : 2009-06-04T18:08:39.025690112 to 2009-06-04T20:39:50.034283520 (0 days 00:06:05.434966016 before mission_end) WARNING 2025-06-26 15:03:33,210 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 00:06:05.434966016 INFO 2025-06-26 15:03:33,211 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-06-04T18:08:52.674755072 to 2009-06-04T20:45:55.469249536 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:03:33,213 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-06-04T18:08:52.384774912 to 2009-06-04T20:45:55.419252992 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 15:03:33,214 resample.py get_mission_start_end():1145 [1] isus : 2009-06-04T18:09:56.470384896 to 2009-06-04T20:45:54.259332352 (0 days 00:00:01.209917184 before mission_end) INFO 2025-06-26 15:03:33,215 resample.py get_mission_start_end():1145 [1] biolume : 2009-06-04T18:08:33.136059392 to 2009-06-04T20:45:54.089309696 (0 days 00:00:01.379939840 before mission_end) INFO 2025-06-26 15:03:33,217 resample.py get_mission_start_end():1145 [1] tailcone : 2009-06-04T18:08:39.315670272 to 2009-06-04T20:45:54.819293952 (0 days 00:00:00.649955584 before mission_end) INFO 2025-06-26 15:03:33,217 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_align.nc mission netCDF file INFO 2025-06-26 15:03:33,218 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,341 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,364 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,386 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,408 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,429 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,429 resample.py resample_variable():1038 [1] Padding hs2_bbp420 with 0 days 00:06:05.434966016 of NaNs to the end of mission INFO 2025-06-26 15:03:33,452 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,452 resample.py resample_variable():1038 [1] Padding hs2_bbp700 with 0 days 00:06:05.434966016 of NaNs to the end of mission INFO 2025-06-26 15:03:33,473 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,473 resample.py resample_variable():1038 [1] Padding hs2_fl700 with 0 days 00:06:05.434966016 of NaNs to the end of mission INFO 2025-06-26 15:03:33,493 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,511 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,534 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,553 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,571 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,590 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,608 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,628 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,649 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,671 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,692 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,717 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,737 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,757 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,777 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,790 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,802 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,813 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,825 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,839 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:03:33,988 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_1S.nc INFO 2025-06-26 15:03:35,386 create_products.py gulper_odv():401 [1] No gulper times found for 2009.155.03 INFO 2025-06-26 15:03:35,386 process.py archive():337 [1] Archiving steps for 2009.155.03 INFO 2025-06-26 15:03:35,386 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03, BASE_PATH = /data/auv_data INFO 2025-06-26 15:03:35,388 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:03:35,389 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.155.03_1S.nc INFO 2025-06-26 15:03:35,405 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:03:35,406 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.155.03_cal.nc INFO 2025-06-26 15:03:35,450 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:03:35,451 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.155.03_align.nc INFO 2025-06-26 15:03:35,490 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:03:35,507 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,522 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,528 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,543 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,576 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,582 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,596 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,603 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,631 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,637 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009155/2009.155.03 done. INFO 2025-06-26 15:03:35,637 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:03:35,637 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.155.03/dorado_2009.155.03_processing.log /Volumes/AUVCTD/surveys/2009/netcdf