INFO 2025-06-26 20:04:48,416 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:04:48,416 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:04:48,416 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.295.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:04:48,416 process.py download_process():165 [1] Download and processing steps for 2013.295.01 INFO 2025-06-26 20:04:48,416 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013295/2013.295.01 INFO 2025-06-26 20:04:48,416 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013295/2013.295.01 to /data/auv_data/dorado/missionlogs/2013.295.01 INFO 2025-06-26 20:04:52,221 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.295.01 INFO 2025-06-26 20:04:52,222 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/ctdDriver.log (4724166 bytes) INFO 2025-06-26 20:04:52,553 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/ctdDriver2.log (4724255 bytes) INFO 2025-06-26 20:04:52,902 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/gps.log (43916 bytes) INFO 2025-06-26 20:04:52,915 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/hydroscatlog.log (4139458 bytes) INFO 2025-06-26 20:04:53,343 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/navigation.log (16723510 bytes) INFO 2025-06-26 20:04:54,505 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/parosci.log (5812070 bytes) INFO 2025-06-26 20:04:54,995 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/tailCone.log (2959387 bytes) INFO 2025-06-26 20:04:55,361 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/biolume.log (3445910 bytes) INFO 2025-06-26 20:04:55,693 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:04:55,867 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.65 seconds INFO 2025-06-26 20:04:55,867 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.295.01/lopc.bin (41581143 bytes) INFO 2025-06-26 20:04:55,867 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:04:55 2025 INFO 2025-06-26 20:04:55,867 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.295.01/parosci.nc INFO 2025-06-26 20:04:55,867 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:04:55,867 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.295.01/parosci.nc INFO 2025-06-26 20:04:55,871 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382468196.6, sensor_off_time = 1382480525.2 INFO 2025-06-26 20:04:55,871 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 12328 seconds. Expecting to read 24656 L frames from the lopc.bin file. INFO 2025-06-26 20:04:55,871 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 24656 records from the lopc.bin file. INFO 2025-06-26 20:04:56,017 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-22 18:56:36 Z and endTime = 2013-10-22 22:22:05 Z with 24656 records expected to be read from lopc.bin INFO 2025-06-26 20:04:56,017 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.295.01/lopc.bin INFO 2025-06-26 20:04:56,017 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.295.01/lopc.nc INFO 2025-06-26 20:04:56,017 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.295.01/lopc.nc INFO 2025-06-26 20:04:56,018 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.295.01 INFO 2025-06-26 20:04:56,018 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:04:56,110 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:04:56,110 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:04:56,110 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:04:56,141 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:04:56,142 process.py calibrate():227 [1] Calibration steps for 2013.295.01 INFO 2025-06-26 20:04:56,279 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:04:56,281 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:04:56,781 calibrate.py _nudge_pos():1806 [1] 82: 0.030 -0.0007096 0.0002440 1905 6.35 -16.570 7.125 2013-10-22T19:04:16.269357568 INFO 2025-06-26 20:04:57,157 calibrate.py _nudge_pos():1806 [1] 122: 0.030 -0.0023215 0.0009387 9165 30.55 -11.265 5.694 2013-10-22T19:35:28.271116800 INFO 2025-06-26 20:04:57,537 calibrate.py _nudge_pos():1806 [1] 163: 0.030 -0.0011639 0.0022446 8560 28.53 -6.048 14.579 2013-10-22T20:04:40.271096576 INFO 2025-06-26 20:04:57,622 calibrate.py _nudge_pos():1806 [1] 172: 0.030 0.0000191 0.0000283 75 0.25 11.503 21.273 2013-10-22T20:05:03.269520896 INFO 2025-06-26 20:04:58,001 calibrate.py _nudge_pos():1806 [1] 212: 0.030 -0.0004629 0.0004090 1460 4.86 -14.110 15.584 2013-10-22T20:10:34.276845568 INFO 2025-06-26 20:04:58,532 calibrate.py _nudge_pos():1806 [1] 269: 0.030 0.0001646 0.0004284 4250 14.16 1.723 5.605 2013-10-22T20:25:40.274780160 INFO 2025-06-26 20:04:58,996 calibrate.py _nudge_pos():1806 [1] 319: 0.030 -0.0004566 -0.0000101 4195 13.98 -4.842 -0.133 2013-10-22T20:40:28.273948160 INFO 2025-06-26 20:04:59,460 calibrate.py _nudge_pos():1806 [1] 369: 0.030 -0.0006858 -0.0002635 6235 20.78 -4.892 -2.350 2013-10-22T21:02:04.275165952 INFO 2025-06-26 20:04:59,733 calibrate.py _nudge_pos():1806 [1] 398: 0.040 -0.0007323 -0.0001189 6730 22.43 -4.839 -0.982 2013-10-22T21:24:58.271041024 INFO 2025-06-26 20:05:00,120 calibrate.py _nudge_pos():1806 [1] 438: 0.040 -0.0009801 -0.0003671 7395 24.65 -5.893 -2.760 2013-10-22T21:50:16.277050368 INFO 2025-06-26 20:05:00,408 calibrate.py _nudge_pos():1806 [1] 469: 0.050 -0.0007409 -0.0003421 5400 18.00 -6.100 -3.522 2013-10-22T22:08:46.271010560 INFO 2025-06-26 20:05:00,763 calibrate.py _nudge_pos():1806 [1] 507: 0.050 -0.0003268 -0.0002659 3355 11.18 -4.331 -4.407 2013-10-22T22:20:34.272509184 INFO 2025-06-26 20:05:01,626 calibrate.py _nudge_pos():1862 [1] 562: - - - 5 0.01 - - INFO 2025-06-26 20:05:01,626 calibrate.py _nudge_pos():1868 [1] Points in final series = 61475 INFO 2025-06-26 20:05:02,281 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:02,749 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:03,125 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:03,127 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.295.01/ctd1.nc INFO 2025-06-26 20:05:03,128 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:05:03,128 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:05:03,129 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:05:03,570 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:03,944 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:05:03,946 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.295.01/ctd2.nc INFO 2025-06-26 20:05:03,947 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:05:03,947 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:05:03,948 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:05:03,948 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.295.01 INFO 2025-06-26 20:05:03,958 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:05:04,476 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 20:05:04,595 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:05:15,684 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.295.01 ERROR 2025-06-26 20:05:15,684 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.295.01 INFO 2025-06-26 20:05:15,736 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_cal.nc INFO 2025-06-26 20:05:15,839 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:05:15,845 process.py align():251 [1] Alignment steps for 2013.295.01 INFO 2025-06-26 20:05:15,879 align.py process_cal():139 [1] Processing dorado_2013.295.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.295.01 INFO 2025-06-26 20:05:15,900 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:05:15,903 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:05:15,948 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:05:15,952 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:05:15,998 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:05:16,001 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:05:16,027 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:05:16,028 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:05:16,044 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:05:16,048 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:05:16,093 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,096 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,135 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,138 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,177 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,180 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,220 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,223 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,263 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,266 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,305 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,308 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,347 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,350 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,388 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,392 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,431 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,434 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,473 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,476 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,516 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,519 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,558 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,561 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,601 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,604 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,642 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,645 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,684 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,688 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,727 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,731 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,772 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,775 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,815 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,819 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,860 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,864 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,904 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,908 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,949 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,952 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:16,993 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.295.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:05:16,996 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:05:17,051 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:05:17,089 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:05:17,149 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:05:17,466 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:05:17,499 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_align.nc INFO 2025-06-26 20:05:17,600 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:05:17,602 process.py resample():273 [1] Resampling steps for 2013.295.01 INFO 2025-06-26 20:05:17,603 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:05:17,631 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_align.nc mission netCDF file INFO 2025-06-26 20:05:17,636 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_align.nc mission netCDF file INFO 2025-06-26 20:05:17,637 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-22T18:57:10.488525568 to 2013-10-22T22:22:05.276274944 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:05:17,639 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-22T18:56:42.700429312 to 2013-10-22T22:22:05.066289408 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 20:05:17,640 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-22T18:57:04.908907776 to 2013-10-22T22:22:05.116285696 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 20:05:17,642 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-22T18:57:04.638926336 to 2013-10-22T22:22:05.116285696 (0 days 00:00:00.159989248 before mission_end) INFO 2025-06-26 20:05:17,643 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-22T18:56:35.280903424 to 2013-10-22T22:22:04.366302976 (0 days 00:00:00.909971968 before mission_end) INFO 2025-06-26 20:05:17,645 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-22T18:56:36.610846208 to 2013-10-22T22:22:05.206279680 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 20:05:17,645 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_align.nc mission netCDF file INFO 2025-06-26 20:05:17,646 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,790 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,816 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,841 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,865 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,889 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,911 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,933 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,954 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:17,977 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,003 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,026 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,046 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,066 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,086 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,106 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,125 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,145 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,167 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,188 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,210 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,231 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,253 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,273 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,294 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,305 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,316 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:18,320 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:05:18,320 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:05:18,762 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:05:18,839 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:05:18,883 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:05:18,902 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:05:18,920 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:05:18,920 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:05:18,953 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:05:19,127 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_1S.nc INFO 2025-06-26 20:05:22,928 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:05:32,074 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.295.01/dorado_2013.295.01_1S_Gulper.txt INFO 2025-06-26 20:05:32,075 process.py archive():337 [1] Archiving steps for 2013.295.01 INFO 2025-06-26 20:05:32,075 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:05:32,076 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:05:32,077 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.295.01_1S.nc INFO 2025-06-26 20:05:32,093 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:05:32,094 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.295.01_cal.nc INFO 2025-06-26 20:05:32,184 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:05:32,185 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.295.01_align.nc INFO 2025-06-26 20:05:32,301 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:05:32,319 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,336 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,340 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,357 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,402 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,421 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,436 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,471 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,477 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013295/2013.295.01 done. INFO 2025-06-26 20:05:32,477 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:05:32,478 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.295.01_1S_Gulper.txt INFO 2025-06-26 20:05:32,483 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.295.01/dorado_2013.295.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:05:32,483 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.295.01/dorado_2013.295.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf