INFO 2025-06-26 19:46:56,059 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 19:46:56,059 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:46:56,059 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.262.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:46:56,059 process.py download_process():165 [1] Download and processing steps for 2013.262.01 INFO 2025-06-26 19:46:56,059 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013262/2013.262.01 INFO 2025-06-26 19:46:56,059 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013262/2013.262.01 to /data/auv_data/dorado/missionlogs/2013.262.01 INFO 2025-06-26 19:46:59,561 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.262.01 INFO 2025-06-26 19:46:59,562 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/ctdDriver.log (5012166 bytes) INFO 2025-06-26 19:46:59,909 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/ctdDriver2.log (5012063 bytes) INFO 2025-06-26 19:47:00,264 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.262.01/ctdDriver2.log: [1] INFO 2025-06-26 19:47:00,279 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/gps.log (64364 bytes) INFO 2025-06-26 19:47:00,294 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/hydroscatlog.log (4389862 bytes) INFO 2025-06-26 19:47:00,730 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.262.01/hydroscatlog.log: [74] INFO 2025-06-26 19:47:00,742 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/navigation.log (17742966 bytes) INFO 2025-06-26 19:47:01,981 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/isuslog.log (397429 bytes) INFO 2025-06-26 19:47:02,024 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/parosci.log (6162614 bytes) INFO 2025-06-26 19:47:02,533 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.262.01/parosci.log: [257 258 259] INFO 2025-06-26 19:47:02,550 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/tailCone.log (3139051 bytes) INFO 2025-06-26 19:47:02,936 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/biolume.log (3655218 bytes) INFO 2025-06-26 19:47:03,294 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:47:03,475 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.91 seconds INFO 2025-06-26 19:47:03,475 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.01/lopc.bin (27102436 bytes) INFO 2025-06-26 19:47:03,475 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:47:03 2025 INFO 2025-06-26 19:47:03,475 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.262.01/parosci.nc INFO 2025-06-26 19:47:03,476 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:47:03,476 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.262.01/parosci.nc INFO 2025-06-26 19:47:03,479 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1379611341.5, sensor_off_time = 1379624417.7 INFO 2025-06-26 19:47:03,479 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 13076 seconds. Expecting to read 26152 L frames from the lopc.bin file. INFO 2025-06-26 19:47:03,479 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 26152 records from the lopc.bin file. INFO 2025-06-26 19:47:03,632 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-09-19 17:22:21 Z and endTime = 2013-09-19 21:00:17 Z with 26152 records expected to be read from lopc.bin INFO 2025-06-26 19:47:03,632 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.262.01/lopc.bin INFO 2025-06-26 19:47:03,632 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.262.01/lopc.nc INFO 2025-06-26 19:47:03,632 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.262.01/lopc.nc INFO 2025-06-26 19:47:03,633 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.262.01 INFO 2025-06-26 19:47:03,633 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:47:03,636 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:47:03,708 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:47:03,708 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:47:03,708 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:47:03,892 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:47:03,893 process.py calibrate():227 [1] Calibration steps for 2013.262.01 INFO 2025-06-26 19:47:04,039 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 19:47:04,041 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:47:04,631 calibrate.py _nudge_pos():1806 [1] 90: 0.100 0.0007953 0.0013687 6690 22.30 5.288 11.375 2013-09-19T17:46:04.809007360 INFO 2025-06-26 19:47:04,968 calibrate.py _nudge_pos():1806 [1] 126: 0.110 0.0010527 0.0018368 8855 29.51 5.289 11.532 2013-09-19T18:16:10.805288192 INFO 2025-06-26 19:47:05,353 calibrate.py _nudge_pos():1806 [1] 167: 0.100 -0.0008960 0.0011896 8890 29.63 -4.485 7.440 2013-09-19T18:46:28.810746368 INFO 2025-06-26 19:47:05,737 calibrate.py _nudge_pos():1806 [1] 208: 0.110 0.0000167 0.0000584 15 0.05 53.102 231.857 2013-09-19T18:47:12.807732224 INFO 2025-06-26 19:47:05,861 calibrate.py _nudge_pos():1806 [1] 221: 0.110 -0.0005448 -0.0013942 13640 45.46 -1.777 -5.683 2013-09-19T19:32:52.810029312 INFO 2025-06-26 19:47:05,872 calibrate.py _nudge_pos():1806 [1] 222: 0.110 -0.0000117 0.0000071 175 0.58 -2.999 2.280 2013-09-19T19:33:27.807631872 INFO 2025-06-26 19:47:06,326 calibrate.py _nudge_pos():1806 [1] 270: 0.120 -0.0007376 -0.0008761 9670 32.23 -3.393 -5.037 2013-09-19T20:06:28.811923712 INFO 2025-06-26 19:47:06,364 calibrate.py _nudge_pos():1806 [1] 274: 0.130 -0.0000302 -0.0000025 145 0.48 -9.339 -0.958 2013-09-19T20:07:00.809731840 INFO 2025-06-26 19:47:06,716 calibrate.py _nudge_pos():1806 [1] 311: 0.120 -0.0010593 -0.0010093 9170 30.56 -5.138 -6.119 2013-09-19T20:38:10.811627776 INFO 2025-06-26 19:47:07,111 calibrate.py _nudge_pos():1806 [1] 353: 0.130 -0.0002719 -0.0003129 3785 12.61 -3.196 -4.597 2013-09-19T20:51:28.806961664 INFO 2025-06-26 19:47:12,120 calibrate.py _nudge_pos():1862 [1] 847: - - - 5 0.01 - - INFO 2025-06-26 19:47:12,120 calibrate.py _nudge_pos():1868 [1] Points in final series = 65223 INFO 2025-06-26 19:47:20,647 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 3 of 52247 INFO 2025-06-26 19:47:21,060 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:47:21,568 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:47:21,964 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:47:21,966 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.262.01/ctd1.nc INFO 2025-06-26 19:47:21,967 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 19:47:21,967 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 19:47:21,967 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:47:24,845 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:47:25,231 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:47:25,233 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.262.01/ctd2.nc WARNING 2025-06-26 19:47:25,234 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (2186) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 19:47:25,234 calibrate.py _range_qc_combined_nc():898 [1] Setting 2186 ctd2_salinity values to NaN INFO 2025-06-26 19:47:25,235 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 19:47:25,235 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:47:25,260 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:47:25,890 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62] INFO 2025-06-26 19:47:26,004 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 19:47:37,826 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.262.01 ERROR 2025-06-26 19:47:37,826 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.262.01 INFO 2025-06-26 19:47:37,879 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_cal.nc INFO 2025-06-26 19:47:40,363 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 19:47:40,368 process.py align():251 [1] Alignment steps for 2013.262.01 INFO 2025-06-26 19:47:40,402 align.py process_cal():139 [1] Processing dorado_2013.262.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.262.01 INFO 2025-06-26 19:47:40,423 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:47:40,426 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:47:40,473 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:47:40,478 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:47:40,527 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:47:40,531 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:47:40,560 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:47:40,560 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:47:40,578 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:47:40,582 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:47:40,629 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,633 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,674 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,678 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,721 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,724 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,766 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,770 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,813 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,817 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,858 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,862 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,905 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,909 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,950 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:40,954 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:40,997 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,001 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,043 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,047 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,091 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,095 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,137 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,140 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,183 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,187 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,229 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,232 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,276 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,279 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,321 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,325 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,369 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,373 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,415 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,419 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,463 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,466 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,510 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,514 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,558 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,562 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,605 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:47:41,609 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:47:41,664 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:47:41,704 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:47:41,746 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:47:41,788 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:47:41,830 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:47:41,894 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:47:42,234 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:47:42,270 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_align.nc INFO 2025-06-26 19:47:42,384 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 19:47:42,387 process.py resample():273 [1] Resampling steps for 2013.262.01 INFO 2025-06-26 19:47:42,387 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:47:42,420 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_align.nc mission netCDF file INFO 2025-06-26 19:47:42,426 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_align.nc mission netCDF file INFO 2025-06-26 19:47:42,427 resample.py get_mission_start_end():1145 [1] navigation: 2013-09-19T17:22:53.434323200 to 2013-09-19T21:00:17.810722048 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:47:42,429 resample.py get_mission_start_end():1145 [1] hs2 : 2013-09-19T17:22:29.255979520 to 2013-09-19T21:00:17.660732416 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 19:47:42,430 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-09-19T17:22:47.844706048 to 2013-09-19T21:00:17.650733312 (0 days 00:00:00.159988736 before mission_end) INFO 2025-06-26 19:47:42,432 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-09-19T17:22:47.844706048 to 2013-09-19T21:00:17.610735872 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 19:47:42,433 resample.py get_mission_start_end():1145 [1] isus : 2013-09-19T17:23:54.890113024 to 2013-09-19T21:00:17.120769536 (0 days 00:00:00.689952512 before mission_end) INFO 2025-06-26 19:47:42,435 resample.py get_mission_start_end():1145 [1] biolume : 2013-09-19T17:22:18.926652928 to 2013-09-19T21:00:17.260725760 (0 days 00:00:00.549996288 before mission_end) INFO 2025-06-26 19:47:42,436 resample.py get_mission_start_end():1145 [1] tailcone : 2013-09-19T17:22:19.706633728 to 2013-09-19T21:00:17.790723584 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 19:47:42,437 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_align.nc mission netCDF file INFO 2025-06-26 19:47:42,437 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,592 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,622 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,650 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,678 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,703 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,728 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,752 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,776 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,798 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,821 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,843 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,866 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,888 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,911 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,933 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,955 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:42,978 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,002 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,026 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,055 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,078 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,102 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,126 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,149 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,163 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,176 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,189 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,200 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,211 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:43,215 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:47:43,215 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:47:43,671 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:47:43,751 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:47:43,797 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:47:43,818 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:47:43,837 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:47:43,837 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:47:43,868 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:47:44,052 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_1S.nc INFO 2025-06-26 19:47:45,722 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:47:56,440 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.262.01/dorado_2013.262.01_1S_Gulper.txt INFO 2025-06-26 19:47:56,440 process.py archive():337 [1] Archiving steps for 2013.262.01 INFO 2025-06-26 19:47:56,440 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01, BASE_PATH = /data/auv_data INFO 2025-06-26 19:47:56,442 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:47:56,443 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.262.01_1S.nc INFO 2025-06-26 19:47:56,460 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:47:56,461 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.262.01_cal.nc INFO 2025-06-26 19:47:56,550 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:47:56,551 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.262.01_align.nc INFO 2025-06-26 19:47:56,674 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:47:56,693 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,710 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,715 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,730 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,789 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,795 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,815 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,830 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,866 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,872 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.01 done. INFO 2025-06-26 19:47:56,872 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:47:56,873 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.262.01_1S_Gulper.txt INFO 2025-06-26 19:47:56,877 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.262.01/dorado_2013.262.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:47:56,877 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.01/dorado_2013.262.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf