INFO 2025-06-26 20:06:18,852 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 20:06:18,852 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:06:18,852 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.296.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:06:18,852 process.py download_process():165 [1] Download and processing steps for 2013.296.01 INFO 2025-06-26 20:06:18,853 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013296/2013.296.01 INFO 2025-06-26 20:06:18,853 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013296/2013.296.01 to /data/auv_data/dorado/missionlogs/2013.296.01 INFO 2025-06-26 20:06:21,939 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.296.01 INFO 2025-06-26 20:06:21,939 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/ctdDriver.log (5380518 bytes) INFO 2025-06-26 20:06:22,314 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/ctdDriver2.log (5379743 bytes) INFO 2025-06-26 20:06:22,699 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/gps.log (80564 bytes) INFO 2025-06-26 20:06:22,716 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/hydroscatlog.log (4711750 bytes) INFO 2025-06-26 20:06:23,198 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/navigation.log (19048838 bytes) INFO 2025-06-26 20:06:24,536 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/parosci.log (6618662 bytes) INFO 2025-06-26 20:06:25,079 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.296.01/parosci.log: [2 3 4 5 6 8 9] INFO 2025-06-26 20:06:25,096 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/tailCone.log (3368587 bytes) INFO 2025-06-26 20:06:25,509 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/biolume.log (3922746 bytes) INFO 2025-06-26 20:06:25,888 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:06:26,091 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.15 seconds INFO 2025-06-26 20:06:26,091 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.296.01/lopc.bin (41353117 bytes) INFO 2025-06-26 20:06:26,091 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:06:26 2025 INFO 2025-06-26 20:06:26,091 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.296.01/parosci.nc INFO 2025-06-26 20:06:26,091 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:06:26,091 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.296.01/parosci.nc INFO 2025-06-26 20:06:26,095 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382549642.0, sensor_off_time = 1382563677.7 INFO 2025-06-26 20:06:26,095 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 14035 seconds. Expecting to read 28070 L frames from the lopc.bin file. INFO 2025-06-26 20:06:26,095 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 28070 records from the lopc.bin file. INFO 2025-06-26 20:06:26,260 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-23 17:34:02 Z and endTime = 2013-10-23 21:27:57 Z with 28070 records expected to be read from lopc.bin INFO 2025-06-26 20:06:26,260 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.296.01/lopc.bin INFO 2025-06-26 20:06:26,260 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.296.01/lopc.nc INFO 2025-06-26 20:06:26,260 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.296.01/lopc.nc INFO 2025-06-26 20:06:26,261 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.296.01 INFO 2025-06-26 20:06:26,261 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:06:26,264 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:06:26,340 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:06:26,340 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:06:26,340 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:06:26,384 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:06:26,385 process.py calibrate():227 [1] Calibration steps for 2013.296.01 INFO 2025-06-26 20:06:26,532 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 20:06:26,534 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:06:27,079 calibrate.py _nudge_pos():1806 [1] 85: 0.070 -0.0007329 0.0016315 7350 24.50 -4.434 12.341 2013-10-23T17:59:52.415244288 INFO 2025-06-26 20:06:27,420 calibrate.py _nudge_pos():1806 [1] 121: 0.070 -0.0007928 0.0022867 8705 29.01 -4.050 14.605 2013-10-23T18:29:28.413580288 INFO 2025-06-26 20:06:27,532 calibrate.py _nudge_pos():1806 [1] 132: 0.070 -0.0000001 -0.0000031 25 0.08 -0.122 -7.107 2013-10-23T18:29:43.412552704 INFO 2025-06-26 20:06:27,775 calibrate.py _nudge_pos():1806 [1] 158: 0.070 -0.0007460 0.0022883 8230 27.43 -4.032 15.458 2013-10-23T18:57:34.418080768 INFO 2025-06-26 20:06:28,071 calibrate.py _nudge_pos():1806 [1] 189: 0.070 -0.0004458 0.0005633 2188 7.30 -9.058 14.304 2013-10-23T19:05:22.416020992 INFO 2025-06-26 20:06:28,475 calibrate.py _nudge_pos():1806 [1] 232: 0.080 0.0002920 0.0003795 4350 14.50 2.987 4.851 2013-10-23T19:20:34.413544704 INFO 2025-06-26 20:06:28,953 calibrate.py _nudge_pos():1806 [1] 283: 0.080 -0.0005130 -0.0000319 4700 15.66 -4.855 -0.378 2013-10-23T19:37:04.415725056 INFO 2025-06-26 20:06:29,282 calibrate.py _nudge_pos():1806 [1] 318: 0.080 -0.0007226 -0.0003237 5500 18.33 -5.844 -3.272 2013-10-23T19:55:58.418040576 INFO 2025-06-26 20:06:29,667 calibrate.py _nudge_pos():1806 [1] 359: 0.090 -0.0008990 -0.0003492 7240 24.13 -5.522 -2.682 2013-10-23T20:20:46.416105472 INFO 2025-06-26 20:06:29,968 calibrate.py _nudge_pos():1806 [1] 391: 0.090 -0.0011470 -0.0004889 7525 25.08 -6.777 -3.612 2013-10-23T20:46:22.410882816 INFO 2025-06-26 20:06:30,274 calibrate.py _nudge_pos():1806 [1] 423: 0.090 -0.0009445 -0.0003942 5485 18.28 -7.656 -3.996 2013-10-23T21:05:10.413609216 INFO 2025-06-26 20:06:30,615 calibrate.py _nudge_pos():1806 [1] 459: 0.090 -0.0003928 -0.0002799 3424 11.41 -5.100 -4.544 2013-10-23T21:17:10.414285824 INFO 2025-06-26 20:06:36,791 calibrate.py _nudge_pos():1862 [1] 1073: - - - 1 0.00 - - INFO 2025-06-26 20:06:36,791 calibrate.py _nudge_pos():1868 [1] Points in final series = 70023 INFO 2025-06-26 20:06:39,536 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:06:40,134 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:06:40,554 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:06:40,557 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.296.01/ctd1.nc INFO 2025-06-26 20:06:40,558 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:06:40,558 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 20:06:40,558 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:06:41,060 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:06:41,504 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:06:41,506 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.296.01/ctd2.nc INFO 2025-06-26 20:06:41,508 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:06:41,508 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 20:06:41,508 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:06:41,508 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.296.01 INFO 2025-06-26 20:06:41,519 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:06:42,110 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63] INFO 2025-06-26 20:06:42,233 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:06:54,943 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.296.01 ERROR 2025-06-26 20:06:54,943 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.296.01 INFO 2025-06-26 20:06:54,999 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_cal.nc INFO 2025-06-26 20:06:55,112 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 20:06:55,117 process.py align():251 [1] Alignment steps for 2013.296.01 INFO 2025-06-26 20:06:55,151 align.py process_cal():139 [1] Processing dorado_2013.296.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.296.01 INFO 2025-06-26 20:06:55,174 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:55,177 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:55,226 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:55,229 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:55,279 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:55,283 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:55,312 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:06:55,312 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:06:55,331 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:06:55,335 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:55,383 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,387 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,430 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,433 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,479 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,482 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,526 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,530 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,574 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,578 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,621 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,624 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,669 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,673 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,716 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,719 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,763 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,767 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,810 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,813 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,857 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,861 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,905 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,908 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:55,954 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:55,957 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,001 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,004 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,050 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,053 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,098 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,102 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,147 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,151 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,194 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,198 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,243 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,247 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,290 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,294 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,338 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,342 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,385 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.296.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:06:56,388 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:06:56,445 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:06:56,488 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:06:56,556 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:06:56,914 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:06:56,950 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_align.nc INFO 2025-06-26 20:06:57,059 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 20:06:57,062 process.py resample():273 [1] Resampling steps for 2013.296.01 INFO 2025-06-26 20:06:57,062 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:06:57,093 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_align.nc mission netCDF file INFO 2025-06-26 20:06:57,098 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_align.nc mission netCDF file INFO 2025-06-26 20:06:57,099 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-23T17:34:32.479366912 to 2013-10-23T21:27:57.609949952 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 20:06:57,100 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-23T17:34:11.700790528 to 2013-10-23T21:27:57.619949056 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 20:06:57,102 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-23T17:34:28.219658752 to 2013-10-23T21:27:57.669945600 (0 days 00:00:00.109992704 before mission_end) INFO 2025-06-26 20:06:57,103 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-23T17:34:29.219590400 to 2013-10-23T21:27:57.659946496 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 20:06:57,105 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-23T17:33:59.201612544 to 2013-10-23T21:27:56.569986816 (0 days 00:00:01.209951488 before mission_end) INFO 2025-06-26 20:06:57,106 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-23T17:34:04.381291776 to 2013-10-23T21:27:57.779938304 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:06:57,107 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_align.nc mission netCDF file INFO 2025-06-26 20:06:57,107 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,265 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,293 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,321 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,348 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,373 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,396 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,420 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,443 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,464 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,487 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,510 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,532 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,554 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,576 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,599 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,622 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,644 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,669 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,694 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,718 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,742 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,766 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,789 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,813 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,825 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,836 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:57,840 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:06:57,840 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:06:58,349 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:06:58,444 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:06:58,494 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:06:58,516 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:06:58,535 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:06:58,535 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:06:58,568 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:06:58,752 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_1S.nc INFO 2025-06-26 20:07:00,483 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:07:12,218 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.296.01/dorado_2013.296.01_1S_Gulper.txt INFO 2025-06-26 20:07:12,219 process.py archive():337 [1] Archiving steps for 2013.296.01 INFO 2025-06-26 20:07:12,219 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:07:12,220 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:07:12,221 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.296.01_1S.nc INFO 2025-06-26 20:07:12,239 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:07:12,240 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.296.01_cal.nc INFO 2025-06-26 20:07:12,339 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:07:12,340 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.296.01_align.nc INFO 2025-06-26 20:07:12,475 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:07:12,496 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,514 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,519 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,589 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,612 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,627 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,666 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,672 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013296/2013.296.01 done. INFO 2025-06-26 20:07:12,672 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:07:12,673 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.296.01_1S_Gulper.txt INFO 2025-06-26 20:07:12,677 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.296.01/dorado_2013.296.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:07:12,678 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.296.01/dorado_2013.296.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf