INFO 2025-06-26 19:28:43,860 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 19:28:43,860 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - inbound mission, Gulper 0 fired on .01 mission and Gulpers 1 through 6 fired on .02 - ctdToUse = ctd1 INFO 2025-06-26 19:28:43,860 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.076.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:28:43,860 process.py download_process():165 [1] Download and processing steps for 2013.076.02 INFO 2025-06-26 19:28:43,860 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013076/2013.076.02 INFO 2025-06-26 19:28:43,861 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013076/2013.076.02 to /data/auv_data/dorado/missionlogs/2013.076.02 INFO 2025-06-26 19:28:46,211 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.076.02 INFO 2025-06-26 19:28:46,211 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/ctdDriver.log (4064454 bytes) INFO 2025-06-26 19:28:46,498 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/ctdDriver2.log (4064351 bytes) INFO 2025-06-26 19:28:46,787 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/gps.log (175604 bytes) INFO 2025-06-26 19:28:46,814 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/hydroscatlog.log (3562630 bytes) INFO 2025-06-26 19:28:47,179 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/navigation.log (14381318 bytes) INFO 2025-06-26 19:28:48,181 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/isuslog.log (313845 bytes) INFO 2025-06-26 19:28:48,215 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/parosci.log (4314518 bytes) INFO 2025-06-26 19:28:48,576 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/tailCone.log (2546635 bytes) INFO 2025-06-26 19:28:48,889 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/biolume.log (2965950 bytes) INFO 2025-06-26 19:28:49,174 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:28:49,324 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.11 seconds INFO 2025-06-26 19:28:49,325 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.076.02/lopc.bin (38407916 bytes) INFO 2025-06-26 19:28:49,325 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:28:49 2025 INFO 2025-06-26 19:28:49,325 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.076.02/parosci.nc INFO 2025-06-26 19:28:49,325 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:28:49,325 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.076.02/parosci.nc INFO 2025-06-26 19:28:49,328 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363538232.6, sensor_off_time = 1363548843.1 INFO 2025-06-26 19:28:49,328 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 10610 seconds. Expecting to read 21220 L frames from the lopc.bin file. INFO 2025-06-26 19:28:49,328 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 21220 records from the lopc.bin file. INFO 2025-06-26 19:28:49,451 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-17 16:37:12 Z and endTime = 2013-03-17 19:34:03 Z with 21220 records expected to be read from lopc.bin INFO 2025-06-26 19:28:49,451 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.076.02/lopc.bin INFO 2025-06-26 19:28:49,451 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.076.02/lopc.nc INFO 2025-06-26 19:28:49,452 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.076.02/lopc.nc INFO 2025-06-26 19:28:49,452 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.076.02 INFO 2025-06-26 19:28:49,452 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:28:49,456 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:28:49,590 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:28:49,590 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:28:49,590 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:28:49,657 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:28:49,657 process.py calibrate():227 [1] Calibration steps for 2013.076.02 INFO 2025-06-26 19:28:49,784 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 19:28:49,786 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:28:50,419 calibrate.py _nudge_pos():1806 [1] 98: 0.180 0.0089247 -0.0034460 10175 33.91 40.639 -18.829 2013-03-17T17:12:43.910162176 INFO 2025-06-26 19:28:50,991 calibrate.py _nudge_pos():1806 [1] 160: 0.180 0.0042506 -0.0013916 10055 33.51 19.581 -7.694 2013-03-17T17:47:15.908220416 INFO 2025-06-26 19:28:51,656 calibrate.py _nudge_pos():1806 [1] 232: 0.190 0.0033641 -0.0004757 9395 31.31 16.581 -2.815 2013-03-17T18:19:45.904636672 INFO 2025-06-26 19:28:52,182 calibrate.py _nudge_pos():1806 [1] 289: 0.190 0.0022604 -0.0002843 8575 28.58 12.204 -1.843 2013-03-17T18:49:16.913314304 INFO 2025-06-26 19:28:52,764 calibrate.py _nudge_pos():1806 [1] 352: 0.200 0.0006882 -0.0009358 1515 5.05 21.041 -34.360 2013-03-17T18:55:21.908310528 INFO 2025-06-26 19:28:53,309 calibrate.py _nudge_pos():1806 [1] 410: 0.200 0.0002099 -0.0003967 644 2.14 15.109 -34.293 2013-03-17T18:58:27.905568512 INFO 2025-06-26 19:28:53,885 calibrate.py _nudge_pos():1806 [1] 472: 0.190 0.0001037 -0.0001007 595 1.98 8.079 -9.424 2013-03-17T19:01:27.913237248 INFO 2025-06-26 19:29:12,105 calibrate.py _nudge_pos():1862 [1] 2389: - - - 5 0.01 - - INFO 2025-06-26 19:29:12,105 calibrate.py _nudge_pos():1868 [1] Points in final series = 51179 WARNING 2025-06-26 19:29:12,176 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:29:12,577 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:29:12,977 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:29:13,287 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:29:13,289 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.076.02/ctd1.nc INFO 2025-06-26 19:29:13,290 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:29:13,290 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 19:29:13,291 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:29:13,669 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:29:13,981 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:29:13,983 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.076.02/ctd2.nc INFO 2025-06-26 19:29:13,984 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:29:13,984 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 19:29:13,984 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:29:14,006 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:29:14,532 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 19:29:14,626 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:29:24,189 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.076.02 ERROR 2025-06-26 19:29:24,189 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.076.02 INFO 2025-06-26 19:29:24,232 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_cal.nc INFO 2025-06-26 19:29:24,327 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 19:29:24,332 process.py align():251 [1] Alignment steps for 2013.076.02 INFO 2025-06-26 19:29:24,365 align.py process_cal():139 [1] Processing dorado_2013.076.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.076.02 INFO 2025-06-26 19:29:24,383 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:29:24,385 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:29:24,427 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:29:24,430 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:29:24,472 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:29:24,476 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:29:24,498 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:29:24,498 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:29:24,514 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:29:24,517 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:29:24,557 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,561 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,596 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,599 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,635 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,638 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,673 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,677 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,714 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,718 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,753 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,757 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,793 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,796 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,831 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,834 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,870 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,874 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,908 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,912 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,948 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,951 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:24,986 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:24,990 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,028 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,031 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,066 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,069 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,106 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,110 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,146 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,150 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,187 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,190 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,226 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,229 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,265 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,269 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,304 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,308 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,344 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,348 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,383 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.076.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:29:25,386 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:29:25,430 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:29:25,463 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:29:25,496 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:29:25,531 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:29:25,566 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:29:25,617 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:29:25,896 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:29:25,926 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_align.nc INFO 2025-06-26 19:29:26,028 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 19:29:26,030 process.py resample():273 [1] Resampling steps for 2013.076.02 INFO 2025-06-26 19:29:26,031 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:29:26,061 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_align.nc mission netCDF file INFO 2025-06-26 19:29:26,066 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_align.nc mission netCDF file INFO 2025-06-26 19:29:26,067 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-17T16:37:50.523568896 to 2013-03-17T19:34:03.109297152 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 19:29:26,069 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-17T16:37:18.665751552 to 2013-03-17T19:34:02.969306624 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 19:29:26,070 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-17T16:37:40.354265600 to 2013-03-17T19:34:02.869313792 (0 days 00:00:00.249982720 before mission_end) INFO 2025-06-26 19:29:26,071 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-17T16:37:40.764237312 to 2013-03-17T19:34:03.019303424 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 19:29:26,073 resample.py get_mission_start_end():1145 [1] isus : 2013-03-17T16:38:27.841012480 to 2013-03-17T19:34:02.839315712 (0 days 00:00:00.279980800 before mission_end) INFO 2025-06-26 19:29:26,074 resample.py get_mission_start_end():1145 [1] biolume : 2013-03-17T16:37:11.996174080 to 2013-03-17T19:34:02.119330816 (0 days 00:00:00.999965696 before mission_end) INFO 2025-06-26 19:29:26,075 resample.py get_mission_start_end():1145 [1] tailcone : 2013-03-17T16:37:14.326048512 to 2013-03-17T19:34:03.119296512 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:29:26,076 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_align.nc mission netCDF file INFO 2025-06-26 19:29:26,076 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,212 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,236 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,259 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,282 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,304 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,324 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,345 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,365 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,384 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,403 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,422 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,441 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,460 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,479 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,497 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,516 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,535 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,556 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,577 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,598 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,618 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,639 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,660 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,680 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,694 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,706 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,717 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,727 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,737 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:26,741 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:29:26,741 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:29:27,100 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:29:27,168 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:29:27,207 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:29:27,224 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:29:27,240 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:29:27,240 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:29:27,268 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:29:27,437 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_1S.nc INFO 2025-06-26 19:29:30,367 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:29:38,824 create_products.py gulper_odv():522 [1] Wrote 6 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.076.02/dorado_2013.076.02_1S_Gulper.txt INFO 2025-06-26 19:29:38,824 process.py archive():337 [1] Archiving steps for 2013.076.02 INFO 2025-06-26 19:29:38,824 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02, BASE_PATH = /data/auv_data INFO 2025-06-26 19:29:38,825 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:29:38,826 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.076.02_1S.nc INFO 2025-06-26 19:29:38,841 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:29:38,843 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.076.02_cal.nc INFO 2025-06-26 19:29:38,917 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:29:38,918 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.076.02_align.nc INFO 2025-06-26 19:29:39,023 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:29:39,038 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,053 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,058 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,072 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,111 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,116 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,132 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,146 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,176 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,182 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013076/2013.076.02 done. INFO 2025-06-26 19:29:39,182 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:29:39,183 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.076.02_1S_Gulper.txt INFO 2025-06-26 19:29:39,188 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.076.02/dorado_2013.076.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:29:39,188 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.076.02/dorado_2013.076.02_processing.log /Volumes/AUVCTD/surveys/2013/netcdf