INFO 2025-06-26 19:50:27,407 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 19:50:27,407 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON September 2013 in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 19:50:27,407 process.py process_mission():449 [1] Processing CANON September 2013 mission 2013.274.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:50:27,407 process.py download_process():165 [1] Download and processing steps for 2013.274.00 INFO 2025-06-26 19:50:27,407 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013274/2013.274.00 INFO 2025-06-26 19:50:27,407 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013274/2013.274.00 to /data/auv_data/dorado/missionlogs/2013.274.00 INFO 2025-06-26 19:50:30,928 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.274.00 INFO 2025-06-26 19:50:30,928 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/ctdDriver.log (2675622 bytes) INFO 2025-06-26 19:50:31,117 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/ctdDriver2.log (2675615 bytes) INFO 2025-06-26 19:50:31,310 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/gps.log (44348 bytes) INFO 2025-06-26 19:50:31,323 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/hydroscatlog.log (2346478 bytes) INFO 2025-06-26 19:50:31,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/navigation.log (9464918 bytes) INFO 2025-06-26 19:50:32,240 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/isuslog.log (212757 bytes) INFO 2025-06-26 19:50:32,264 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/parosci.log (3300854 bytes) INFO 2025-06-26 19:50:32,541 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/tailCone.log (1678891 bytes) INFO 2025-06-26 19:50:32,749 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/biolume.log (1955762 bytes) INFO 2025-06-26 19:50:32,944 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:50:33,048 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.12 seconds INFO 2025-06-26 19:50:33,049 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.274.00/lopc.bin (17104678 bytes) INFO 2025-06-26 19:50:33,049 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:50:33 2025 INFO 2025-06-26 19:50:33,049 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.274.00/parosci.nc INFO 2025-06-26 19:50:33,049 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:50:33,049 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.274.00/parosci.nc INFO 2025-06-26 19:50:33,052 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1380639319.8, sensor_off_time = 1380646312.1 INFO 2025-06-26 19:50:33,052 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 6992 seconds. Expecting to read 13984 L frames from the lopc.bin file. INFO 2025-06-26 19:50:33,052 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 13984 records from the lopc.bin file. INFO 2025-06-26 19:50:33,134 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-01 14:55:19 Z and endTime = 2013-10-01 16:51:52 Z with 13984 records expected to be read from lopc.bin INFO 2025-06-26 19:50:33,135 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.274.00/lopc.bin INFO 2025-06-26 19:50:33,135 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.274.00/lopc.nc INFO 2025-06-26 19:50:33,135 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.274.00/lopc.nc INFO 2025-06-26 19:50:33,135 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.274.00 INFO 2025-06-26 19:50:33,136 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:50:33,138 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:50:33,170 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:50:33,170 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:50:33,170 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:50:33,264 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:50:33,265 process.py calibrate():227 [1] Calibration steps for 2013.274.00 INFO 2025-06-26 19:50:33,375 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 19:50:33,376 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:50:33,837 calibrate.py _nudge_pos():1806 [1] 78: 0.070 0.0000649 0.0000460 600 2.00 4.818 4.266 2013-10-01T14:58:33.839028736 INFO 2025-06-26 19:50:34,710 calibrate.py _nudge_pos():1806 [1] 173: 0.080 0.0001362 0.0012752 9126 30.43 0.663 7.765 2013-10-01T15:30:33.837499904 INFO 2025-06-26 19:50:35,610 calibrate.py _nudge_pos():1806 [1] 270: 0.080 0.0002918 0.0013839 9450 31.50 1.373 8.141 2013-10-01T16:03:39.831450112 INFO 2025-06-26 19:50:36,520 calibrate.py _nudge_pos():1806 [1] 368: 0.090 0.0004811 0.0013112 8905 29.68 2.402 8.186 2013-10-01T16:34:57.832797952 INFO 2025-06-26 19:50:37,366 calibrate.py _nudge_pos():1806 [1] 459: 0.090 0.0004892 0.0002960 3900 13.00 5.579 4.220 2013-10-01T16:49:27.833199104 INFO 2025-06-26 19:50:38,716 calibrate.py _nudge_pos():1862 [1] 568: - - - 1 0.00 - - INFO 2025-06-26 19:50:38,716 calibrate.py _nudge_pos():1868 [1] Points in final series = 34789 INFO 2025-06-26 19:50:39,107 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:50:39,382 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:50:39,589 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:50:39,591 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.274.00/ctd1.nc INFO 2025-06-26 19:50:39,592 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:50:39,592 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 19:50:39,592 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:50:39,847 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:50:40,060 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:50:40,062 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.274.00/ctd2.nc INFO 2025-06-26 19:50:40,063 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:50:40,063 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 19:50:40,063 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:50:40,085 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:50:40,381 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 85 86 87 88 89 90 91 92] INFO 2025-06-26 19:50:40,445 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:50:46,777 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.274.00 ERROR 2025-06-26 19:50:46,777 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.274.00 INFO 2025-06-26 19:50:46,807 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_cal.nc INFO 2025-06-26 19:50:46,895 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 19:50:46,901 process.py align():251 [1] Alignment steps for 2013.274.00 INFO 2025-06-26 19:50:46,931 align.py process_cal():139 [1] Processing dorado_2013.274.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.274.00 INFO 2025-06-26 19:50:46,944 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:46,947 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:46,977 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:46,979 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:47,008 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:47,011 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:47,028 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:50:47,028 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:50:47,041 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:50:47,044 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:47,072 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,075 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,101 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,104 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,130 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,132 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,160 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,163 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,190 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,193 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,220 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,222 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,249 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,252 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,279 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,283 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,309 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,312 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,340 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,342 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,370 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,373 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,399 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,402 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,429 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,432 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,458 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,461 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,488 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,492 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,519 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,522 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,551 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,554 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,580 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,583 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,610 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,613 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,640 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,643 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,670 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,673 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,701 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.274.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:50:47,703 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:50:47,737 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.97 INFO 2025-06-26 19:50:47,765 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.97 INFO 2025-06-26 19:50:47,792 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.97 INFO 2025-06-26 19:50:47,820 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:50:47,849 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:50:47,887 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:50:48,078 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:50:48,102 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_align.nc INFO 2025-06-26 19:50:48,186 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 19:50:48,188 process.py resample():273 [1] Resampling steps for 2013.274.00 INFO 2025-06-26 19:50:48,189 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:50:48,217 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_align.nc mission netCDF file INFO 2025-06-26 19:50:48,223 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_align.nc mission netCDF file INFO 2025-06-26 19:50:48,224 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-01T14:55:53.640003328 to 2013-10-01T16:51:52.033320704 (0 days 00:00:00.049996288 before mission_end) INFO 2025-06-26 19:50:48,226 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-01T14:55:27.931764480 to 2013-10-01T16:51:51.893330176 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 19:50:48,227 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-01T14:55:46.480493568 to 2013-10-01T16:51:52.083316992 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:50:48,228 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-01T14:55:46.210512128 to 2013-10-01T16:51:52.053319168 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 19:50:48,230 resample.py get_mission_start_end():1145 [1] isus : 2013-10-01T14:57:14.374472448 to 2013-10-01T16:51:51.883330816 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 19:50:48,231 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-01T14:55:19.012340992 to 2013-10-01T16:51:50.933361664 (0 days 00:00:01.149955328 before mission_end) INFO 2025-06-26 19:50:48,232 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-01T14:55:18.482411520 to 2013-10-01T16:51:51.943326720 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 19:50:48,233 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_align.nc mission netCDF file INFO 2025-06-26 19:50:48,233 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,327 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,345 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,363 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,380 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,397 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,413 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,429 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,444 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,458 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,472 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,486 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,500 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,513 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,528 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,542 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,556 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,570 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,586 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,601 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,616 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,631 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,645 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,660 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,675 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,686 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,696 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,706 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,715 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,723 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:48,726 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:50:48,726 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:50:48,979 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:50:49,024 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:50:49,049 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:50:49,060 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:50:49,071 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:50:49,072 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:50:49,094 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:50:49,241 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_1S.nc INFO 2025-06-26 19:50:50,933 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:51:01,734 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.274.00/dorado_2013.274.00_1S_Gulper.txt INFO 2025-06-26 19:51:01,734 process.py archive():337 [1] Archiving steps for 2013.274.00 INFO 2025-06-26 19:51:01,735 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:51:01,735 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:51:01,736 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.274.00_1S.nc INFO 2025-06-26 19:51:01,748 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:51:01,749 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.274.00_cal.nc INFO 2025-06-26 19:51:01,802 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:51:01,803 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.274.00_align.nc INFO 2025-06-26 19:51:01,878 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:51:01,892 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,905 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,909 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,919 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,945 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,951 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,964 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,975 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:01,998 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:02,004 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013274/2013.274.00 done. INFO 2025-06-26 19:51:02,004 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:51:02,005 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.274.00_1S_Gulper.txt INFO 2025-06-26 19:51:02,010 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.274.00/dorado_2013.274.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:51:02,010 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.274.00/dorado_2013.274.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf