INFO 2025-06-26 20:03:59,500 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 20:03:59,500 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:03:59,500 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.295.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:03:59,500 process.py download_process():165 [1] Download and processing steps for 2013.295.00 INFO 2025-06-26 20:03:59,500 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013295/2013.295.00 INFO 2025-06-26 20:03:59,500 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013295/2013.295.00 to /data/auv_data/dorado/missionlogs/2013.295.00 INFO 2025-06-26 20:04:02,914 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.295.00 INFO 2025-06-26 20:04:02,914 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/ctdDriver.log (3257766 bytes) INFO 2025-06-26 20:04:03,155 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/ctdDriver2.log (3264287 bytes) INFO 2025-06-26 20:04:03,387 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/gps.log (146228 bytes) INFO 2025-06-26 20:04:03,410 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/hydroscatlog.log (2862406 bytes) INFO 2025-06-26 20:04:03,719 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/navigation.log (11548710 bytes) INFO 2025-06-26 20:04:04,541 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/parosci.log (4025030 bytes) INFO 2025-06-26 20:04:04,872 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.295.00/parosci.log: [20] INFO 2025-06-26 20:04:04,884 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/tailCone.log (2046427 bytes) INFO 2025-06-26 20:04:05,141 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/biolume.log (2384034 bytes) INFO 2025-06-26 20:04:05,375 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:04:05,498 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.58 seconds INFO 2025-06-26 20:04:05,498 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.00/lopc.bin (23142355 bytes) INFO 2025-06-26 20:04:05,498 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:04:05 2025 INFO 2025-06-26 20:04:05,498 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.295.00/parosci.nc INFO 2025-06-26 20:04:05,498 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:04:05,498 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.295.00/parosci.nc INFO 2025-06-26 20:04:05,501 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382454086.4, sensor_off_time = 1382462610.2 INFO 2025-06-26 20:04:05,501 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 8523 seconds. Expecting to read 17046 L frames from the lopc.bin file. INFO 2025-06-26 20:04:05,501 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 17046 records from the lopc.bin file. INFO 2025-06-26 20:04:05,603 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-22 15:01:26 Z and endTime = 2013-10-22 17:23:30 Z with 17046 records expected to be read from lopc.bin INFO 2025-06-26 20:04:05,604 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.295.00/lopc.bin INFO 2025-06-26 20:04:05,604 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.295.00/lopc.nc INFO 2025-06-26 20:04:05,604 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.295.00/lopc.nc INFO 2025-06-26 20:04:05,604 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.295.00 INFO 2025-06-26 20:04:05,605 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:04:05,642 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:04:05,642 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:04:05,643 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:04:08,686 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:04:08,687 process.py calibrate():227 [1] Calibration steps for 2013.295.00 INFO 2025-06-26 20:04:08,801 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 20:04:08,803 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:04:09,390 calibrate.py _nudge_pos():1806 [1] 94: 0.080 0.0002220 0.0000548 1030 3.43 9.585 2.958 2013-10-22T15:06:22.187199232 INFO 2025-06-26 20:04:09,933 calibrate.py _nudge_pos():1806 [1] 153: 0.080 0.0001713 0.0014810 9550 31.83 0.797 8.622 2013-10-22T15:39:10.192381696 INFO 2025-06-26 20:04:10,451 calibrate.py _nudge_pos():1806 [1] 209: 0.100 0.0001583 0.0010793 9414 31.38 0.747 6.373 2013-10-22T16:11:28.189619712 INFO 2025-06-26 20:04:11,011 calibrate.py _nudge_pos():1806 [1] 269: 0.100 0.0002728 0.0007049 7775 25.91 1.560 5.041 2013-10-22T16:38:22.189053184 INFO 2025-06-26 20:04:11,517 calibrate.py _nudge_pos():1806 [1] 323: 0.100 0.0002269 0.0003346 4775 15.91 2.112 3.897 2013-10-22T16:55:10.190000384 INFO 2025-06-26 20:04:11,536 calibrate.py _nudge_pos():1806 [1] 325: 0.090 -0.0000092 0.0000338 25 0.08 -16.966 78.338 2013-10-22T16:55:16.189589504 INFO 2025-06-26 20:04:27,366 calibrate.py _nudge_pos():1862 [1] 1982: - - - 5 0.01 - - INFO 2025-06-26 20:04:27,366 calibrate.py _nudge_pos():1868 [1] Points in final series = 42449 INFO 2025-06-26 20:04:29,043 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:04:29,374 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:04:29,625 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 41 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:04:29,627 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.295.00/ctd1.nc INFO 2025-06-26 20:04:29,628 calibrate.py _range_qc_combined_nc():898 [1] Setting 59 ctd1_salinity values to NaN INFO 2025-06-26 20:04:29,628 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 20:04:29,628 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:04:29,935 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:04:30,190 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:04:30,192 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.295.00/ctd2.nc INFO 2025-06-26 20:04:30,193 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:04:30,194 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 20:04:30,194 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:04:30,194 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.295.00 INFO 2025-06-26 20:04:30,201 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:04:30,556 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75] INFO 2025-06-26 20:04:30,631 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:04:38,251 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.295.00 ERROR 2025-06-26 20:04:38,251 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.295.00 INFO 2025-06-26 20:04:38,287 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_cal.nc INFO 2025-06-26 20:04:38,368 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, 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_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_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 20:04:38,373 process.py align():251 [1] Alignment steps for 2013.295.00 INFO 2025-06-26 20:04:38,401 align.py process_cal():139 [1] Processing dorado_2013.295.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.295.00 INFO 2025-06-26 20:04:38,417 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:04:38,419 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:04:38,454 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:04:38,458 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:04:38,492 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:04:38,495 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:04:38,514 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:04:38,514 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:04:38,527 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:04:38,530 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:04:38,563 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,565 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,595 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,598 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,628 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,630 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,660 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,663 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,693 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,696 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,726 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,729 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,759 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,762 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,791 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,794 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,824 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,826 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,856 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,858 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,888 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,891 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,921 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,923 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,953 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,956 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:38,986 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:38,988 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,020 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,023 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,053 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,056 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,086 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,089 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,119 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,122 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,153 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,156 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,186 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,189 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,220 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,223 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,255 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:04:39,258 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:04:39,299 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:04:39,329 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:04:39,372 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:04:39,597 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:04:39,623 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_align.nc INFO 2025-06-26 20:04:39,707 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, 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_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_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 20:04:39,709 process.py resample():273 [1] Resampling steps for 2013.295.00 INFO 2025-06-26 20:04:39,710 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:04:39,737 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_align.nc mission netCDF file INFO 2025-06-26 20:04:39,742 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_align.nc mission netCDF file INFO 2025-06-26 20:04:39,743 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-22T15:02:00.195146752 to 2013-10-22T17:23:30.193542144 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 20:04:39,744 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-22T15:01:30.197201920 to 2013-10-22T17:23:30.213540864 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:04:39,746 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-22T15:02:07.894619392 to 2013-10-22T17:23:30.183543040 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 20:04:39,747 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-22T15:01:51.285757184 to 2013-10-22T17:23:30.053551616 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 20:04:39,748 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-22T15:01:23.837603328 to 2013-10-22T17:23:29.643545600 (0 days 00:00:00.569995264 before mission_end) INFO 2025-06-26 20:04:39,750 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-22T15:01:24.277607424 to 2013-10-22T17:23:30.043552512 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 20:04:39,750 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_align.nc mission netCDF file INFO 2025-06-26 20:04:39,751 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,858 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,878 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,897 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,917 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,936 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,953 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,971 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:39,989 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,007 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,025 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,042 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,059 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,076 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,093 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,109 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,125 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,140 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,158 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,176 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,193 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,211 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,228 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,245 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,263 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,273 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,282 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,286 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:04:40,286 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:04:40,594 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:04:40,646 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:04:40,678 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:04:40,692 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:04:40,706 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:04:40,706 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:04:40,730 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:04:40,881 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_1S.nc INFO 2025-06-26 20:04:42,914 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:04:48,096 create_products.py gulper_odv():522 [1] Wrote 5 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.295.00/dorado_2013.295.00_1S_Gulper.txt INFO 2025-06-26 20:04:48,096 process.py archive():337 [1] Archiving steps for 2013.295.00 INFO 2025-06-26 20:04:48,096 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:04:48,096 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:04:48,098 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.295.00_1S.nc INFO 2025-06-26 20:04:48,111 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:04:48,112 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.295.00_cal.nc INFO 2025-06-26 20:04:48,170 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:04:48,171 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.295.00_align.nc INFO 2025-06-26 20:04:48,257 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:04:48,271 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,285 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,290 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,302 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,332 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,347 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,358 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,382 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,387 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.00 done. INFO 2025-06-26 20:04:48,387 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:04:48,388 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.295.00_1S_Gulper.txt INFO 2025-06-26 20:04:48,392 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.295.00/dorado_2013.295.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:04:48,392 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.00/dorado_2013.295.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf