INFO 2025-06-26 19:34:59,549 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 19:34:59,549 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Molecular Ecology - August 2013 - North Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:34:59,549 process.py process_mission():449 [1] Processing SIMZ August 2013 mission 2013.226.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:34:59,549 process.py download_process():165 [1] Download and processing steps for 2013.226.01 INFO 2025-06-26 19:34:59,549 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013226/2013.226.01 INFO 2025-06-26 19:34:59,549 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013226/2013.226.01 to /data/auv_data/dorado/missionlogs/2013.226.01 INFO 2025-06-26 19:35:02,970 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.226.01 INFO 2025-06-26 19:35:02,971 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/ctdDriver.log (4490406 bytes) INFO 2025-06-26 19:35:03,289 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/ctdDriver2.log (4490399 bytes) INFO 2025-06-26 19:35:03,614 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/gps.log (437828 bytes) INFO 2025-06-26 19:35:03,667 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/hydroscatlog.log (3932314 bytes) INFO 2025-06-26 19:35:04,076 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/navigation.log (15877318 bytes) INFO 2025-06-26 19:35:05,199 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/isuslog.log (347765 bytes) INFO 2025-06-26 19:35:05,236 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.226.01/isuslog.log: [ 1 2 3 4 5 7 8 9 10 11 12 13 14 15 16 18 19 20 21] INFO 2025-06-26 19:35:05,237 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/parosci.log (5530886 bytes) INFO 2025-06-26 19:35:05,713 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/tailCone.log (2810635 bytes) INFO 2025-06-26 19:35:06,059 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/biolume.log (3273238 bytes) INFO 2025-06-26 19:35:06,380 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:35:06,543 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.57 seconds INFO 2025-06-26 19:35:06,544 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.226.01/lopc.bin (35446395 bytes) INFO 2025-06-26 19:35:06,544 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:35:06 2025 INFO 2025-06-26 19:35:06,544 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.226.01/parosci.nc INFO 2025-06-26 19:35:06,544 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:35:06,544 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.226.01/parosci.nc INFO 2025-06-26 19:35:06,547 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1376492237.7, sensor_off_time = 1376503947.3 INFO 2025-06-26 19:35:06,547 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11709 seconds. Expecting to read 23418 L frames from the lopc.bin file. INFO 2025-06-26 19:35:06,547 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 23418 records from the lopc.bin file. INFO 2025-06-26 19:35:06,684 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-08-14 14:57:17 Z and endTime = 2013-08-14 18:12:27 Z with 23418 records expected to be read from lopc.bin INFO 2025-06-26 19:35:06,684 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.226.01/lopc.bin INFO 2025-06-26 19:35:06,684 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.226.01/lopc.nc INFO 2025-06-26 19:35:06,686 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.226.01/lopc.nc INFO 2025-06-26 19:35:06,686 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.226.01 INFO 2025-06-26 19:35:06,686 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:35:06,747 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:35:06,747 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:35:06,747 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:35:06,878 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:35:06,878 process.py calibrate():227 [1] Calibration steps for 2013.226.01 INFO 2025-06-26 19:35:07,087 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 19:35:07,089 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:35:07,677 calibrate.py _nudge_pos():1806 [1] 94: 0.180 0.0001901 -0.0002248 490 1.63 17.267 -25.550 2013-08-14T15:00:26.960347136 INFO 2025-06-26 19:35:07,716 calibrate.py _nudge_pos():1806 [1] 98: 0.180 0.0000166 0.0000183 65 0.21 11.537 15.918 2013-08-14T15:00:42.959251200 INFO 2025-06-26 19:35:08,192 calibrate.py _nudge_pos():1806 [1] 149: 0.190 0.0083878 -0.0055856 7950 26.50 46.891 -39.062 2013-08-14T15:28:02.956903680 INFO 2025-06-26 19:35:08,642 calibrate.py _nudge_pos():1806 [1] 197: 0.180 0.0062778 -0.0081012 9065 30.21 30.785 -49.685 2013-08-14T15:59:02.959484672 INFO 2025-06-26 19:35:09,034 calibrate.py _nudge_pos():1806 [1] 238: 0.190 0.0031498 -0.0062873 7090 23.63 19.752 -49.303 2013-08-14T16:23:20.959604736 INFO 2025-06-26 19:35:09,583 calibrate.py _nudge_pos():1806 [1] 296: 0.200 0.0004095 -0.0029007 3584 11.94 5.081 -45.004 2013-08-14T16:36:14.956582400 INFO 2025-06-26 19:36:03,962 calibrate.py _nudge_pos():1862 [1] 6031: - - - 0 0.00 - - INFO 2025-06-26 19:36:03,962 calibrate.py _nudge_pos():1868 [1] Points in final series = 56165 INFO 2025-06-26 19:36:04,498 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:04,947 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:36:05,300 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:36:05,302 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.226.01/ctd1.nc INFO 2025-06-26 19:36:05,303 calibrate.py _range_qc_combined_nc():898 [1] Setting 79 ctd1_salinity values to NaN INFO 2025-06-26 19:36:05,303 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 19:36:05,303 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:36:05,728 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:06,076 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:36:06,078 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.226.01/ctd2.nc INFO 2025-06-26 19:36:06,079 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:36:06,079 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 19:36:06,079 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:36:06,607 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:36:07,200 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:36:07,224 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.226.01 ERROR 2025-06-26 19:36:07,224 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.226.01 INFO 2025-06-26 19:36:07,272 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_cal.nc INFO 2025-06-26 19:36:07,376 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, 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 19:36:07,381 process.py align():251 [1] Alignment steps for 2013.226.01 INFO 2025-06-26 19:36:07,415 align.py process_cal():139 [1] Processing dorado_2013.226.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.226.01 INFO 2025-06-26 19:36:07,435 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:07,438 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:07,483 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:07,486 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:07,531 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:07,535 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:07,560 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:36:07,561 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:36:07,577 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:36:07,581 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:07,624 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,628 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,665 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,669 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,708 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,712 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,750 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,753 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,793 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,796 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,834 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,837 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,876 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,879 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,917 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,921 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:07,961 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:07,964 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,002 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,006 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,045 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,049 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,088 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,092 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,131 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,135 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,172 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,176 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,216 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,219 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,258 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,262 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,301 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,305 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,344 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,347 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,387 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,391 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,430 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,433 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,474 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,478 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,516 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.226.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:36:08,520 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:36:08,568 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:36:08,605 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:36:08,642 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:36:08,681 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:36:08,720 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:36:08,779 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:36:09,080 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:36:09,112 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_align.nc INFO 2025-06-26 19:36:09,217 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, 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 19:36:09,220 process.py resample():273 [1] Resampling steps for 2013.226.01 INFO 2025-06-26 19:36:09,220 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:36:09,251 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_align.nc mission netCDF file INFO 2025-06-26 19:36:09,256 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_align.nc mission netCDF file INFO 2025-06-26 19:36:09,258 resample.py get_mission_start_end():1145 [1] navigation: 2013-08-14T14:57:54.660780544 to 2013-08-14T18:12:27.151160064 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:36:09,259 resample.py get_mission_start_end():1145 [1] hs2 : 2013-08-14T14:57:21.953020928 to 2013-08-14T18:12:27.051166720 (0 days 00:00:00.209985792 before mission_end) INFO 2025-06-26 19:36:09,261 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-08-14T14:57:35.292107008 to 2013-08-14T18:12:27.261152512 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:36:09,262 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-08-14T14:57:35.352102912 to 2013-08-14T18:12:27.251153152 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 19:36:09,263 resample.py get_mission_start_end():1145 [1] isus : 2013-08-14T14:58:16.289298688 to 2013-08-14T18:12:27.251153152 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 19:36:09,265 resample.py get_mission_start_end():1145 [1] biolume : 2013-08-14T14:57:15.763410688 to 2013-08-14T18:12:26.201190656 (0 days 00:00:01.059961856 before mission_end) INFO 2025-06-26 19:36:09,266 resample.py get_mission_start_end():1145 [1] tailcone : 2013-08-14T14:57:18.293271808 to 2013-08-14T18:12:27.091164160 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 19:36:09,267 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_align.nc mission netCDF file INFO 2025-06-26 19:36:09,267 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,407 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,434 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,460 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,486 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,509 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,531 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,553 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,574 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,595 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,617 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,638 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,659 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,680 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,701 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,722 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,743 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,763 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,786 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,808 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,830 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,852 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,873 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,895 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,917 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,930 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,943 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,955 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,966 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,976 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:09,981 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:36:09,981 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:36:10,412 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:36:10,489 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:36:10,535 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:36:10,554 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:36:10,571 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:36:10,572 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:36:10,601 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:36:10,776 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_1S.nc INFO 2025-06-26 19:36:13,122 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:36:21,914 create_products.py gulper_odv():522 [1] Wrote 8 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.226.01/dorado_2013.226.01_1S_Gulper.txt INFO 2025-06-26 19:36:21,915 process.py archive():337 [1] Archiving steps for 2013.226.01 INFO 2025-06-26 19:36:21,915 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:36:21,916 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:36:21,917 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.226.01_1S.nc INFO 2025-06-26 19:36:21,932 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:36:21,933 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.226.01_cal.nc INFO 2025-06-26 19:36:22,017 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:36:22,018 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.226.01_align.nc INFO 2025-06-26 19:36:22,133 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:36:22,151 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,166 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,172 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,187 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,228 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,233 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,252 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,266 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,300 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,305 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013226/2013.226.01 done. INFO 2025-06-26 19:36:22,305 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:36:22,306 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.226.01_1S_Gulper.txt INFO 2025-06-26 19:36:22,310 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.226.01/dorado_2013.226.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:36:22,310 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.226.01/dorado_2013.226.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf