INFO 2025-06-26 19:46:20,372 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 19:46:20,372 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:46:20,372 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.262.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:46:20,372 process.py download_process():165 [1] Download and processing steps for 2013.262.00 INFO 2025-06-26 19:46:20,373 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013262/2013.262.00 INFO 2025-06-26 19:46:20,373 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013262/2013.262.00 to /data/auv_data/dorado/missionlogs/2013.262.00 INFO 2025-06-26 19:46:22,889 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.262.00 INFO 2025-06-26 19:46:22,889 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/ctdDriver.log (2708550 bytes) INFO 2025-06-26 19:46:23,088 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/ctdDriver2.log (2708159 bytes) INFO 2025-06-26 19:46:23,289 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/gps.log (57380 bytes) INFO 2025-06-26 19:46:23,303 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/hydroscatlog.log (2374618 bytes) INFO 2025-06-26 19:46:23,556 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/navigation.log (9579430 bytes) INFO 2025-06-26 19:46:24,247 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/isuslog.log (213013 bytes) INFO 2025-06-26 19:46:24,272 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/parosci.log (3341798 bytes) INFO 2025-06-26 19:46:24,550 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.262.00/parosci.log: [2 3 4 5 6 7 8 9] INFO 2025-06-26 19:46:24,560 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/tailCone.log (1699147 bytes) INFO 2025-06-26 19:46:24,779 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/biolume.log (1979334 bytes) INFO 2025-06-26 19:46:24,980 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:46:25,089 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.20 seconds INFO 2025-06-26 19:46:25,089 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.262.00/lopc.bin (17508581 bytes) INFO 2025-06-26 19:46:25,089 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:46:25 2025 INFO 2025-06-26 19:46:25,090 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.262.00/parosci.nc INFO 2025-06-26 19:46:25,090 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:46:25,090 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.262.00/parosci.nc INFO 2025-06-26 19:46:25,093 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1379601636.6, sensor_off_time = 1379608714.0 INFO 2025-06-26 19:46:25,093 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 7077 seconds. Expecting to read 14154 L frames from the lopc.bin file. INFO 2025-06-26 19:46:25,093 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 14154 records from the lopc.bin file. INFO 2025-06-26 19:46:25,177 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-09-19 14:40:36 Z and endTime = 2013-09-19 16:38:33 Z with 14154 records expected to be read from lopc.bin INFO 2025-06-26 19:46:25,177 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.262.00/lopc.bin INFO 2025-06-26 19:46:25,177 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.262.00/lopc.nc INFO 2025-06-26 19:46:25,177 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.262.00/lopc.nc INFO 2025-06-26 19:46:25,178 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.262.00 INFO 2025-06-26 19:46:25,178 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:46:25,181 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:46:25,235 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:46:25,235 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:46:25,235 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:46:25,467 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:46:25,468 process.py calibrate():227 [1] Calibration steps for 2013.262.00 INFO 2025-06-26 19:46:25,582 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 19:46:25,583 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:46:26,188 calibrate.py _nudge_pos():1806 [1] 95: 0.110 0.0000109 -0.0000895 555 1.85 0.875 -8.984 2013-09-19T14:43:58.777491712 INFO 2025-06-26 19:46:26,235 calibrate.py _nudge_pos():1806 [1] 100: 0.100 0.0000290 0.0000086 60 0.20 21.828 8.098 2013-09-19T14:44:14.776396032 INFO 2025-06-26 19:46:26,597 calibrate.py _nudge_pos():1806 [1] 139: 0.110 0.0002395 0.0009235 9270 30.90 1.149 5.539 2013-09-19T15:15:46.776785152 INFO 2025-06-26 19:46:27,103 calibrate.py _nudge_pos():1806 [1] 194: 0.120 0.0003472 0.0007438 9420 31.40 1.639 4.390 2013-09-19T15:48:04.774023168 INFO 2025-06-26 19:46:27,569 calibrate.py _nudge_pos():1806 [1] 244: 0.120 0.0003481 0.0009035 8965 29.88 1.726 5.603 2013-09-19T16:18:46.777837312 INFO 2025-06-26 19:46:27,974 calibrate.py _nudge_pos():1806 [1] 287: 0.130 0.0002917 0.0000658 3240 10.80 4.005 1.129 2013-09-19T16:30:16.770569472 INFO 2025-06-26 19:46:32,627 calibrate.py _nudge_pos():1862 [1] 747: - - - 1 0.00 - - INFO 2025-06-26 19:46:32,628 calibrate.py _nudge_pos():1868 [1] Points in final series = 35210 INFO 2025-06-26 19:46:34,012 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:46:34,297 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:46:34,514 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:46:34,516 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.262.00/ctd1.nc INFO 2025-06-26 19:46:34,517 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 19:46:34,517 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 19:46:34,517 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:46:34,784 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:46:35,000 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:46:35,002 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.262.00/ctd2.nc INFO 2025-06-26 19:46:35,003 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:46:35,003 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 19:46:35,003 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:46:35,020 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:46:35,316 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 124680 347700] INFO 2025-06-26 19:46:35,379 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: 0 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:46:41,772 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.262.00 ERROR 2025-06-26 19:46:41,772 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.262.00 INFO 2025-06-26 19:46:41,803 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_cal.nc INFO 2025-06-26 19:46:41,884 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 19:46:41,890 process.py align():251 [1] Alignment steps for 2013.262.00 INFO 2025-06-26 19:46:41,920 align.py process_cal():139 [1] Processing dorado_2013.262.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.262.00 INFO 2025-06-26 19:46:41,934 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:41,937 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:41,968 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:41,971 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:42,002 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:42,005 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:42,024 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:46:42,024 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:46:42,035 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:46:42,038 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:42,072 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,075 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,103 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,106 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,133 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,135 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,165 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,169 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,200 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,203 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,229 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,232 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,259 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,262 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,289 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,292 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,319 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,322 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,350 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,352 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,380 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,383 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,410 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,413 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,441 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,444 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,472 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,475 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,504 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,508 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,548 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,552 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,592 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,596 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,633 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,636 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,664 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,667 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,695 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,698 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,726 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,729 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,756 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.262.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:46:42,759 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:46:42,793 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.95 INFO 2025-06-26 19:46:42,821 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.95 INFO 2025-06-26 19:46:42,849 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.95 INFO 2025-06-26 19:46:42,878 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:46:42,908 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:46:42,949 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:46:43,143 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:46:43,168 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_align.nc INFO 2025-06-26 19:46:43,269 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 19:46:43,272 process.py resample():273 [1] Resampling steps for 2013.262.00 INFO 2025-06-26 19:46:43,272 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:46:43,305 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_align.nc mission netCDF file INFO 2025-06-26 19:46:43,311 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_align.nc mission netCDF file INFO 2025-06-26 19:46:43,313 resample.py get_mission_start_end():1145 [1] navigation: 2013-09-19T14:41:12.198903296 to 2013-09-19T16:38:33.976508672 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:46:43,314 resample.py get_mission_start_end():1145 [1] hs2 : 2013-09-19T14:40:46.370672640 to 2013-09-19T16:38:33.836518144 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 19:46:43,316 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-09-19T14:41:02.489568512 to 2013-09-19T16:38:33.836518144 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 19:46:43,318 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-09-19T14:41:03.599492608 to 2013-09-19T16:38:33.936511232 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 19:46:43,319 resample.py get_mission_start_end():1145 [1] isus : 2013-09-19T14:41:53.986040832 to 2013-09-19T16:38:33.286555648 (0 days 00:00:00.689953024 before mission_end) INFO 2025-06-26 19:46:43,321 resample.py get_mission_start_end():1145 [1] biolume : 2013-09-19T14:40:36.111341312 to 2013-09-19T16:38:32.866550272 (0 days 00:00:01.109958400 before mission_end) INFO 2025-06-26 19:46:43,322 resample.py get_mission_start_end():1145 [1] tailcone : 2013-09-19T14:40:36.561344512 to 2013-09-19T16:38:33.976508672 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:46:43,323 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_align.nc mission netCDF file INFO 2025-06-26 19:46:43,323 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,421 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,440 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,459 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,478 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,496 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,513 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,530 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,546 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,561 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,576 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,591 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,606 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,622 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,637 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,652 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,667 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,682 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,699 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,716 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,733 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,749 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,766 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,783 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,799 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,811 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,822 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,833 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,842 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,851 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:43,855 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:46:43,855 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:46:44,103 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:46:44,150 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:46:44,177 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:46:44,189 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:46:44,200 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:46:44,200 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:46:44,223 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:46:44,373 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_1S.nc INFO 2025-06-26 19:46:45,993 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:46:55,758 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.262.00/dorado_2013.262.00_1S_Gulper.txt INFO 2025-06-26 19:46:55,758 process.py archive():337 [1] Archiving steps for 2013.262.00 INFO 2025-06-26 19:46:55,758 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:46:55,760 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:46:55,761 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.262.00_1S.nc INFO 2025-06-26 19:46:55,773 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:46:55,774 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.262.00_cal.nc INFO 2025-06-26 19:46:55,829 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:46:55,830 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.262.00_align.nc INFO 2025-06-26 19:46:55,901 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:46:55,915 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:55,927 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:55,931 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:55,943 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:55,972 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:55,978 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:55,992 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:56,004 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:56,026 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:56,031 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013262/2013.262.00 done. INFO 2025-06-26 19:46:56,032 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:46:56,033 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.262.00_1S_Gulper.txt INFO 2025-06-26 19:46:56,037 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.262.00/dorado_2013.262.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:46:56,037 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.262.00/dorado_2013.262.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf