INFO 2025-06-26 19:41:24,245 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 19:41:24,245 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:41:24,245 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.259.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:41:24,245 process.py download_process():165 [1] Download and processing steps for 2013.259.00 INFO 2025-06-26 19:41:24,245 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013259/2013.259.00 INFO 2025-06-26 19:41:24,245 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013259/2013.259.00 to /data/auv_data/dorado/missionlogs/2013.259.00 INFO 2025-06-26 19:41:28,248 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.259.00 INFO 2025-06-26 19:41:28,249 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/ctdDriver.log (9440166 bytes) INFO 2025-06-26 19:41:28,919 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/ctdDriver2.log (9449279 bytes) INFO 2025-06-26 19:41:29,622 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/gps.log (445100 bytes) INFO 2025-06-26 19:41:29,678 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/hydroscatlog.log (8272006 bytes) INFO 2025-06-26 19:41:30,527 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/navigation.log (33452054 bytes) INFO 2025-06-26 19:41:32,886 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/isuslog.log (752757 bytes) INFO 2025-06-26 19:41:32,959 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.259.00/isuslog.log: [1 3] INFO 2025-06-26 19:41:32,961 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/parosci.log (11613158 bytes) INFO 2025-06-26 19:41:33,922 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/tailCone.log (5912011 bytes) INFO 2025-06-26 19:41:34,648 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/biolume.log (6881458 bytes) INFO 2025-06-26 19:41:35,322 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:41:35,657 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.41 seconds INFO 2025-06-26 19:41:35,658 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.259.00/lopc.bin (66770186 bytes) INFO 2025-06-26 19:41:35,658 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:41:35 2025 INFO 2025-06-26 19:41:35,658 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.259.00/parosci.nc INFO 2025-06-26 19:41:35,658 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:41:35,658 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.259.00/parosci.nc INFO 2025-06-26 19:41:35,661 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1379345961.4, sensor_off_time = 1379370592.4 INFO 2025-06-26 19:41:35,662 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 24631 seconds. Expecting to read 49262 L frames from the lopc.bin file. INFO 2025-06-26 19:41:35,662 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 49262 records from the lopc.bin file. INFO 2025-06-26 19:41:35,955 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-09-16 15:39:21 Z and endTime = 2013-09-16 22:29:52 Z with 49262 records expected to be read from lopc.bin INFO 2025-06-26 19:41:35,955 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.259.00/lopc.bin INFO 2025-06-26 19:41:35,955 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.259.00/lopc.nc INFO 2025-06-26 19:41:35,956 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.259.00/lopc.nc INFO 2025-06-26 19:41:35,956 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.259.00 INFO 2025-06-26 19:41:35,956 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:41:36,026 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:41:36,027 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:41:36,027 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:41:36,528 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:41:36,529 process.py calibrate():227 [1] Calibration steps for 2013.259.00 INFO 2025-06-26 19:41:36,736 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 19:41:36,738 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:41:37,569 calibrate.py _nudge_pos():1806 [1] 119: 0.160 0.0080903 -0.0069306 13464 44.88 26.771 -28.615 2013-09-16T16:26:09.983891712 INFO 2025-06-26 19:41:38,233 calibrate.py _nudge_pos():1806 [1] 190: 0.150 0.0059794 -0.0061530 13600 45.33 19.583 -25.152 2013-09-16T17:12:39.992763136 INFO 2025-06-26 19:41:39,144 calibrate.py _nudge_pos():1806 [1] 287: 0.170 0.0042675 -0.0047026 13680 45.60 13.889 -19.111 2013-09-16T17:59:51.988758016 INFO 2025-06-26 19:41:39,929 calibrate.py _nudge_pos():1806 [1] 370: 0.170 0.0028775 -0.0039956 13570 45.23 9.438 -16.369 2013-09-16T18:46:27.987219200 INFO 2025-06-26 19:41:40,700 calibrate.py _nudge_pos():1806 [1] 451: 0.180 0.0023316 -0.0023710 13640 45.46 7.605 -9.664 2013-09-16T19:33:15.984858112 INFO 2025-06-26 19:41:41,300 calibrate.py _nudge_pos():1806 [1] 514: 0.180 0.0027881 -0.0024710 13730 45.76 9.030 -10.005 2013-09-16T20:20:03.992496384 INFO 2025-06-26 19:41:41,979 calibrate.py _nudge_pos():1806 [1] 584: 0.190 0.0010092 -0.0006400 10395 34.65 4.316 -3.423 2013-09-16T20:55:51.985348608 INFO 2025-06-26 19:41:42,000 calibrate.py _nudge_pos():1806 [1] 586: 0.190 0.0000151 0.0000308 234 0.78 2.875 7.347 2013-09-16T20:56:39.992060160 INFO 2025-06-26 19:41:54,394 calibrate.py _nudge_pos():1806 [1] 1850: 0.200 -0.0000063 -0.0000091 24 0.08 -12.108 -22.085 2013-09-16T21:17:47.985196544 INFO 2025-06-26 19:42:24,449 calibrate.py _nudge_pos():1806 [1] 4912: 0.010 -0.0000250 0.0000062 15 0.05 -79.529 24.818 2013-09-16T22:08:53.185216000 INFO 2025-06-26 19:42:36,922 calibrate.py _nudge_pos():1862 [1] 6132: - - - 1 0.00 - - INFO 2025-06-26 19:42:36,922 calibrate.py _nudge_pos():1868 [1] Points in final series = 119434 INFO 2025-06-26 19:42:37,281 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 4 of 98464 INFO 2025-06-26 19:42:38,050 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:42:38,972 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 49 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:42:39,710 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 49 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:42:39,712 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.259.00/ctd1.nc INFO 2025-06-26 19:42:39,713 calibrate.py _range_qc_combined_nc():898 [1] Setting 45 ctd1_salinity values to NaN INFO 2025-06-26 19:42:39,714 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 19:42:39,714 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:42:40,582 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:42:41,307 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:42:41,309 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.259.00/ctd2.nc INFO 2025-06-26 19:42:41,311 calibrate.py _range_qc_combined_nc():898 [1] Setting 30 ctd2_salinity values to NaN INFO 2025-06-26 19:42:41,311 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 19:42:41,311 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:42:42,438 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:42:43,561 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84] INFO 2025-06-26 19:42:43,772 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:43:06,033 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.259.00 ERROR 2025-06-26 19:43:06,034 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.259.00 INFO 2025-06-26 19:43:06,192 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_cal.nc INFO 2025-06-26 19:43:06,362 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 19:43:06,368 process.py align():251 [1] Alignment steps for 2013.259.00 INFO 2025-06-26 19:43:06,410 align.py process_cal():139 [1] Processing dorado_2013.259.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.259.00 INFO 2025-06-26 19:43:06,444 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:43:06,448 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:43:06,533 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:43:06,539 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:43:06,617 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:43:06,623 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:43:06,671 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:43:06,671 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:43:06,701 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:43:06,706 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:43:06,784 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:06,788 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:06,856 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:06,861 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:06,930 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:06,934 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,003 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,008 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,078 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,083 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,151 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,156 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,225 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,229 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,298 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,303 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,372 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,377 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,446 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,452 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,522 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,526 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,594 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,599 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,668 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,673 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,742 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,747 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,816 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,821 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,889 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,894 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:07,965 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:07,970 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:08,039 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:08,044 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:08,114 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:08,119 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:08,187 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:08,192 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:08,263 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:08,268 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:08,339 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.259.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:43:08,343 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:43:08,431 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:43:08,492 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:43:08,553 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.96 INFO 2025-06-26 19:43:08,616 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:43:08,679 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:43:08,787 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:43:09,425 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:43:09,480 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_align.nc INFO 2025-06-26 19:43:09,649 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 19:43:09,651 process.py resample():273 [1] Resampling steps for 2013.259.00 INFO 2025-06-26 19:43:09,652 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:43:09,691 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_align.nc mission netCDF file INFO 2025-06-26 19:43:09,698 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_align.nc mission netCDF file INFO 2025-06-26 19:43:09,699 resample.py get_mission_start_end():1145 [1] navigation: 2013-09-16T15:39:57.003854080 to 2013-09-16T22:29:52.388954624 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:43:09,701 resample.py get_mission_start_end():1145 [1] hs2 : 2013-09-16T15:39:25.705997824 to 2013-09-16T22:29:52.188968448 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 19:43:09,703 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-09-16T15:40:11.152884736 to 2013-09-16T22:29:52.388954624 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:43:09,705 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-09-16T15:39:47.044536320 to 2013-09-16T22:29:52.248964352 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 19:43:09,707 resample.py get_mission_start_end():1145 [1] isus : 2013-09-16T15:40:20.232262656 to 2013-09-16T22:29:51.639006208 (0 days 00:00:00.749948416 before mission_end) INFO 2025-06-26 19:43:09,708 resample.py get_mission_start_end():1145 [1] biolume : 2013-09-16T15:39:19.496389120 to 2013-09-16T22:29:51.518980096 (0 days 00:00:00.869974528 before mission_end) INFO 2025-06-26 19:43:09,710 resample.py get_mission_start_end():1145 [1] tailcone : 2013-09-16T15:39:20.976322048 to 2013-09-16T22:29:52.368956160 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 19:43:09,711 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_align.nc mission netCDF file INFO 2025-06-26 19:43:09,711 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:09,970 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,015 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,059 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,106 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,144 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,182 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,220 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,257 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,292 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,328 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,362 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,396 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,430 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,465 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,499 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,533 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,568 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,606 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,644 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,683 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,719 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,757 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,794 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,832 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,852 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,869 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,885 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,900 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,914 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:10,919 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:43:10,919 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:43:11,818 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:43:11,977 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:43:12,064 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:43:12,103 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:43:12,133 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:43:12,133 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:43:12,180 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:43:12,432 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_1S.nc INFO 2025-06-26 19:43:14,638 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:43:25,861 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.259.00/dorado_2013.259.00_1S_Gulper.txt INFO 2025-06-26 19:43:25,862 process.py archive():337 [1] Archiving steps for 2013.259.00 INFO 2025-06-26 19:43:25,862 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:43:25,863 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:43:25,864 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.259.00_1S.nc INFO 2025-06-26 19:43:25,886 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:43:25,887 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.259.00_cal.nc INFO 2025-06-26 19:43:26,044 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:43:26,045 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.259.00_align.nc INFO 2025-06-26 19:43:26,284 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:43:26,315 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,344 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,350 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,375 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,462 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,471 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,503 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,526 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,597 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,607 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013259/2013.259.00 done. INFO 2025-06-26 19:43:26,607 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:43:26,612 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.259.00_1S_Gulper.txt INFO 2025-06-26 19:43:26,626 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.259.00/dorado_2013.259.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:43:26,626 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.259.00/dorado_2013.259.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf