INFO 2025-06-26 17:59:37,531 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 17:59:37,531 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX mission going back and forth on 36.9 line around weak salinity front - aborted early, maybe because of a trex cron job - ctdToUse = ctd1 INFO 2025-06-26 17:59:37,531 process.py process_mission():449 [1] Processing CANON June 2011 mission 2011.171.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 17:59:37,531 process.py download_process():165 [1] Download and processing steps for 2011.171.01 INFO 2025-06-26 17:59:37,531 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011171/2011.171.01 INFO 2025-06-26 17:59:37,531 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011171/2011.171.01 to /data/auv_data/dorado/missionlogs/2011.171.01 INFO 2025-06-26 17:59:44,070 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.171.01 INFO 2025-06-26 17:59:44,070 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/ctdDriver.log (20767302 bytes) INFO 2025-06-26 17:59:45,618 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/ctdDriver2.log (20767583 bytes) INFO 2025-06-26 17:59:47,289 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/gps.log (2288948 bytes) INFO 2025-06-26 17:59:47,541 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/hydroscatlog.log (18170818 bytes) INFO 2025-06-26 17:59:49,569 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/navigation.log (73535606 bytes) INFO 2025-06-26 17:59:55,487 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/isuslog.log (1720437 bytes) INFO 2025-06-26 17:59:55,666 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/parosci.log (21998774 bytes) INFO 2025-06-26 17:59:57,628 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/tailCone.log (12985627 bytes) INFO 2025-06-26 17:59:59,320 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/biolume.log (15111494 bytes) INFO 2025-06-26 18:00:00,875 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:00:01,659 logs2netcdfs.py download_process_logs():807 [1] Time to process: 17.59 seconds INFO 2025-06-26 18:00:01,660 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.171.01/lopc.bin (122376528 bytes) INFO 2025-06-26 18:00:01,660 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:00:01 2025 INFO 2025-06-26 18:00:01,660 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.171.01/parosci.nc INFO 2025-06-26 18:00:01,660 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:00:01,660 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.171.01/parosci.nc INFO 2025-06-26 18:00:01,664 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1308605998.1, sensor_off_time = 1308660104.7 INFO 2025-06-26 18:00:01,665 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 54106 seconds. Expecting to read 108212 L frames from the lopc.bin file. INFO 2025-06-26 18:00:01,665 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 108212 records from the lopc.bin file. INFO 2025-06-26 18:00:02,414 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-06-20 21:39:58 Z and endTime = 2011-06-21 12:41:44 Z with 108212 records expected to be read from lopc.bin INFO 2025-06-26 18:00:02,414 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.171.01/lopc.bin INFO 2025-06-26 18:00:02,414 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.171.01/lopc.nc INFO 2025-06-26 18:00:02,414 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.171.01/lopc.nc INFO 2025-06-26 18:00:02,415 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.171.01 INFO 2025-06-26 18:00:02,415 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 18:00:02,419 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A097551 WARNING 2025-06-26 18:00:02,419 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 18:00:02,471 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 18:00:02,471 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 18:00:02,471 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 18:00:08,577 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 24876 13762 1 0 0 0 0 6.2 seconds, last L Frame: 108212 ERROR 2025-06-26 18:00:13,267 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 18:00:13,269 process.py calibrate():227 [1] Calibration steps for 2011.171.01 INFO 2025-06-26 18:00:13,641 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 18:00:13,643 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:00:20,281 calibrate.py _nudge_pos():1806 [1] 679: 0.130 0.0003817 -0.0027174 9815 32.71 1.729 -15.392 2011-06-20T22:23:58.402239488 INFO 2025-06-26 18:00:21,268 calibrate.py _nudge_pos():1806 [1] 774: 0.140 0.0000987 -0.0027014 9160 30.53 0.479 -16.396 2011-06-20T22:56:04.400299520 INFO 2025-06-26 18:00:22,738 calibrate.py _nudge_pos():1806 [1] 919: 0.140 -0.0004126 -0.0022688 8670 28.90 -2.116 -14.549 2011-06-20T23:27:22.401647616 INFO 2025-06-26 18:00:25,009 calibrate.py _nudge_pos():1806 [1] 1141: 0.140 0.0000179 -0.0026195 8975 29.91 0.089 -16.227 2011-06-21T00:00:58.403542016 INFO 2025-06-26 18:00:25,113 calibrate.py _nudge_pos():1806 [1] 1151: 0.140 -0.0000490 -0.0000800 15 0.05 -155.613 -317.588 2011-06-21T00:01:10.402720000 INFO 2025-06-26 18:00:26,380 calibrate.py _nudge_pos():1806 [1] 1275: 0.150 -0.0002964 -0.0023120 9015 30.05 -1.462 -14.259 2011-06-21T00:33:16.400780288 INFO 2025-06-26 18:00:27,962 calibrate.py _nudge_pos():1806 [1] 1428: 0.150 0.0001215 -0.0025836 9109 30.36 0.593 -15.767 2011-06-21T01:06:10.405551616 INFO 2025-06-26 18:00:29,699 calibrate.py _nudge_pos():1806 [1] 1595: 0.150 -0.0002937 -0.0026038 9190 30.63 -1.421 -15.752 2011-06-21T01:39:34.408268032 INFO 2025-06-26 18:00:31,290 calibrate.py _nudge_pos():1806 [1] 1745: 0.160 -0.0002767 -0.0025718 9335 31.11 -1.318 -15.317 2011-06-21T02:13:10.400163072 INFO 2025-06-26 18:00:32,417 calibrate.py _nudge_pos():1806 [1] 1853: 0.160 -0.0003367 -0.0018431 6335 21.11 -2.363 -16.176 2011-06-21T02:36:04.406037248 INFO 2025-06-26 18:00:41,147 calibrate.py _nudge_pos():1806 [1] 2684: 0.160 -0.0016031 -0.0022824 9740 32.46 -7.318 -13.028 2011-06-21T03:22:22.405731328 INFO 2025-06-26 18:00:42,601 calibrate.py _nudge_pos():1806 [1] 2822: 0.170 0.0000310 -0.0030075 9485 31.61 0.145 -17.628 2011-06-21T03:56:16.406392576 INFO 2025-06-26 18:00:43,788 calibrate.py _nudge_pos():1806 [1] 2933: 0.170 0.0004917 -0.0030436 9830 32.76 2.224 -17.214 2011-06-21T04:30:52.404176896 INFO 2025-06-26 18:00:45,210 calibrate.py _nudge_pos():1806 [1] 3064: 0.170 0.0002777 -0.0006840 3040 10.13 4.063 -12.511 2011-06-21T04:43:10.403620608 INFO 2025-06-26 18:05:55,038 calibrate.py _nudge_pos():1862 [1] 31741: - - - 0 0.00 - - INFO 2025-06-26 18:05:55,038 calibrate.py _nudge_pos():1868 [1] Points in final series = 262757 INFO 2025-06-26 18:05:55,375 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=55) for self.args.mission=2011.171.01 INFO 2025-06-26 18:05:55,382 calibrate.py _depth_process():2175 [1] Setting 190 depths values to NaN WARNING 2025-06-26 18:05:55,389 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:05:55,743 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 2 of 216307 INFO 2025-06-26 18:05:57,375 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:05:59,469 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:06:01,064 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:06:01,068 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.171.01/ctd1.nc INFO 2025-06-26 18:06:01,069 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 18:06:01,070 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 18:06:01,070 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 18:06:02,945 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:06:04,535 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:06:04,539 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.171.01/ctd2.nc INFO 2025-06-26 18:06:04,540 calibrate.py _range_qc_combined_nc():898 [1] Setting 172 ctd2_salinity values to NaN INFO 2025-06-26 18:06:04,541 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 18:06:04,541 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 18:06:04,628 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 18:06:07,518 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 18:06:07,606 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.171.01 ERROR 2025-06-26 18:06:07,606 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.171.01 INFO 2025-06-26 18:06:07,812 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_cal.nc INFO 2025-06-26 18:06:08,144 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 18:06:08,152 process.py align():251 [1] Alignment steps for 2011.171.01 INFO 2025-06-26 18:06:08,226 align.py process_cal():139 [1] Processing dorado_2011.171.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.171.01 INFO 2025-06-26 18:06:08,298 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:06:08,305 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:06:08,473 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:06:08,483 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:06:08,653 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:06:08,665 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:06:08,767 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 18:06:08,767 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 18:06:08,832 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:06:08,842 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:06:09,006 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,015 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:09,159 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,167 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:09,312 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,321 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:09,467 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,475 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:09,628 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,637 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:09,806 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,818 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:09,963 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:09,972 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:10,117 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:10,125 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:10,272 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:10,281 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:10,426 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:10,436 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:10,583 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:10,592 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:10,737 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:10,746 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:10,892 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:10,901 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,045 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,053 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,199 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,208 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,354 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,362 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,509 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,517 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,663 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,671 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,820 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,829 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:11,975 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:11,985 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:12,133 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:12,141 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:12,286 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.171.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:06:12,294 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:06:12,468 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:06:12,582 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:06:12,697 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:06:12,817 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:06:12,938 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:06:13,170 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 18:06:14,547 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:06:14,662 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_align.nc INFO 2025-06-26 18:06:14,973 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 18:06:14,978 process.py resample():273 [1] Resampling steps for 2011.171.01 INFO 2025-06-26 18:06:14,979 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 18:06:15,040 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_align.nc mission netCDF file INFO 2025-06-26 18:06:15,048 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_align.nc mission netCDF file INFO 2025-06-26 18:06:15,050 resample.py get_mission_start_end():1145 [1] navigation: 2011-06-20T21:40:36.010515456 to 2011-06-21T12:41:44.606563072 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 18:06:15,053 resample.py get_mission_start_end():1145 [1] hs2 : 2011-06-20T21:40:03.522740992 to 2011-06-21T12:41:44.656559360 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 18:06:15,055 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-06-20T21:40:25.661224704 to 2011-06-21T12:41:44.496570624 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 18:06:15,058 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-06-20T21:40:25.671223808 to 2011-06-21T12:41:44.686557440 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:06:15,059 resample.py get_mission_start_end():1145 [1] isus : 2011-06-20T21:41:17.487674112 to 2011-06-21T12:41:43.956607488 (0 days 00:00:00.729949952 before mission_end) INFO 2025-06-26 18:06:15,061 resample.py get_mission_start_end():1145 [1] biolume : 2011-06-20T21:39:57.333130752 to 2011-06-21T12:41:44.166558976 (0 days 00:00:00.519998464 before mission_end) INFO 2025-06-26 18:06:15,063 resample.py get_mission_start_end():1145 [1] tailcone : 2011-06-20T21:40:00.032980224 to 2011-06-21T12:41:44.616562432 (0 days 00:00:00.069995008 before mission_end) INFO 2025-06-26 18:06:15,064 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_align.nc mission netCDF file INFO 2025-06-26 18:06:15,065 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:15,608 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:15,704 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:15,791 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:15,879 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:15,954 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,029 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,104 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,175 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,243 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,311 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,379 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,446 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,514 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,581 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,648 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,716 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,784 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,856 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:16,930 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,007 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,081 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,152 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,292 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,365 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,397 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,425 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,452 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,476 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,500 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:17,507 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 18:06:17,508 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 18:06:19,509 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 18:06:20,074 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 18:06:20,288 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 18:06:20,375 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 18:06:20,440 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 18:06:20,440 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 18:06:20,531 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 18:06:20,966 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_1S.nc INFO 2025-06-26 18:06:24,802 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 18:06:28,314 create_products.py gulper_odv():522 [1] Wrote 3 Gulper data lines to /data/auv_data/dorado/missionodvs/2011.171.01/dorado_2011.171.01_1S_Gulper.txt INFO 2025-06-26 18:06:28,314 process.py archive():337 [1] Archiving steps for 2011.171.01 INFO 2025-06-26 18:06:28,315 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01, BASE_PATH = /data/auv_data INFO 2025-06-26 18:06:28,316 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 18:06:28,317 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.171.01_1S.nc INFO 2025-06-26 18:06:28,362 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:06:28,363 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.171.01_cal.nc INFO 2025-06-26 18:06:28,689 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:06:28,691 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.171.01_align.nc INFO 2025-06-26 18:06:29,242 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:06:29,301 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,357 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,368 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,417 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,606 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,616 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,674 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,718 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,856 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,884 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011171/2011.171.01 done. INFO 2025-06-26 18:06:29,884 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 18:06:29,885 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2011/odv/dorado_2011.171.01_1S_Gulper.txt INFO 2025-06-26 18:06:29,890 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2011.171.01/dorado_2011.171.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2011/odv done. INFO 2025-06-26 18:06:29,891 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.171.01/dorado_2011.171.01_processing.log /Volumes/AUVCTD/surveys/2011/netcdf