INFO 2025-06-26 14:31:11,352 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 14:31:11,352 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Kanna trex mission - ctdToUse = ctd1 INFO 2025-06-26 14:31:11,352 process.py process_mission():449 [1] Processing AUVCTD mission 2008.318.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:31:11,352 process.py download_process():165 [1] Download and processing steps for 2008.318.01 INFO 2025-06-26 14:31:11,352 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2008/2008318/2008.318.01 INFO 2025-06-26 14:31:11,353 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2008/2008318/2008.318.01 to /data/auv_data/dorado/missionlogs/2008.318.01 INFO 2025-06-26 14:31:14,717 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2008.318.01 INFO 2025-06-26 14:31:14,718 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/ctdDriver.log (4028156 bytes) INFO 2025-06-26 14:31:15,014 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/ctdDriver2.log (4028237 bytes) INFO 2025-06-26 14:31:15,310 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2008.318.01/ctdDriver2.log: [37205] INFO 2025-06-26 14:31:15,324 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/gps.log (206996 bytes) INFO 2025-06-26 14:31:15,355 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/hydroscatlog.log (3854278 bytes) INFO 2025-06-26 14:31:15,763 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/navigation.log (13508058 bytes) INFO 2025-06-26 14:31:16,791 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/isuslog.log (267477 bytes) INFO 2025-06-26 14:31:16,821 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/parosci.log (4701686 bytes) INFO 2025-06-26 14:31:17,242 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/tailCone.log (591595 bytes) INFO 2025-06-26 14:31:17,322 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/biolume.log (3125420 bytes) INFO 2025-06-26 14:31:17,623 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:31:17,796 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.08 seconds INFO 2025-06-26 14:31:17,797 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2008.318.01/lopc.bin (5508444 bytes) INFO 2025-06-26 14:31:17,797 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:31:17 2025 INFO 2025-06-26 14:31:17,797 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2008.318.01/parosci.nc INFO 2025-06-26 14:31:17,797 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:31:17,797 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2008.318.01/parosci.nc INFO 2025-06-26 14:31:17,800 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1226591050.0, sensor_off_time = 1226602527.7 INFO 2025-06-26 14:31:17,800 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11477 seconds. Expecting to read 22954 L frames from the lopc.bin file. INFO 2025-06-26 14:31:17,801 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22954 records from the lopc.bin file. INFO 2025-06-26 14:31:17,937 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2008-11-13 15:44:10 Z and endTime = 2008-11-13 18:55:27 Z with 22954 records expected to be read from lopc.bin INFO 2025-06-26 14:31:17,937 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2008.318.01/lopc.bin INFO 2025-06-26 14:31:17,937 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2008.318.01/lopc.nc INFO 2025-06-26 14:31:17,938 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2008.318.01/lopc.nc INFO 2025-06-26 14:31:17,938 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2008.318.01 INFO 2025-06-26 14:31:17,939 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:31:17,975 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:31:17,975 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:31:17,975 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 14:31:18,091 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 14:31:18,092 process.py calibrate():227 [1] Calibration steps for 2008.318.01 INFO 2025-06-26 14:31:18,237 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 14:31:18,239 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:31:18,669 calibrate.py _nudge_pos():1806 [1] 72: 0.010 0.0033784 -0.0013105 9260 30.86 16.248 -7.868 2008-11-13T16:16:12.059830272 INFO 2025-06-26 14:31:20,145 calibrate.py _nudge_pos():1806 [1] 227: 0.010 0.0004471 0.0019111 9550 31.83 2.085 11.125 2008-11-13T16:50:36.068435968 INFO 2025-06-26 14:31:21,828 calibrate.py _nudge_pos():1806 [1] 403: 0.020 0.0024958 -0.0021326 9355 31.18 11.881 -12.674 2008-11-13T17:24:42.068275200 INFO 2025-06-26 14:31:23,428 calibrate.py _nudge_pos():1806 [1] 555: 0.020 -0.0022748 0.0028634 9685 32.28 -10.458 16.437 2008-11-13T17:59:30.065237760 INFO 2025-06-26 14:31:23,537 calibrate.py _nudge_pos():1806 [1] 566: 0.020 -0.0000139 -0.0000214 15 0.05 -44.358 -84.807 2008-11-13T17:59:43.064347392 INFO 2025-06-26 14:31:24,936 calibrate.py _nudge_pos():1806 [1] 711: 0.030 -0.0009498 -0.0003262 5245 17.48 -8.063 -3.458 2008-11-13T18:19:36.062621184 INFO 2025-06-26 14:31:45,703 calibrate.py _nudge_pos():1862 [1] 2830: - - - 3 0.01 - - INFO 2025-06-26 14:31:45,703 calibrate.py _nudge_pos():1868 [1] Points in final series = 57205 WARNING 2025-06-26 14:31:45,787 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:31:45,873 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 45872 INFO 2025-06-26 14:31:46,229 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:31:46,668 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:31:47,012 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:31:47,014 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2008.318.01/ctd1.nc INFO 2025-06-26 14:31:47,016 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:31:47,016 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 14:31:47,016 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:31:49,533 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:31:49,881 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 14:31:49,883 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2008.318.01/ctd2.nc INFO 2025-06-26 14:31:49,884 calibrate.py _range_qc_combined_nc():898 [1] Setting 82 ctd2_salinity values to NaN INFO 2025-06-26 14:31:49,885 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 14:31:49,885 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:31:49,907 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:31:50,470 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 240 241 242 243 840 841 842 843 2040 2041 2042 2043 2640 2641 2642 2643 2644 2645 2646 2647 2648 5160 5161 5162 5163 14040 14041 14042 14043 14044 14045 21540 21541 21542 21543 21544 21545 33000 33001 33002 33003 35160 35161 35162 35163 35700 35701 35702 35703 35704 35705 75060 75061 75062 75063 75780 75781 75782 75783 81120 86160 86161 86162 86163 86164 86165 99660 99661 99662 99663 99664 99665 99666 99667 99668 110280 110281 110282 110283 110284 110285 110286 110287 110288 113580 114300 114301 114302 114480 114481 114482 114960 114961 114962 114963 114964 114965 114966 114967 114968 115080 115081 115082 115083 115084 115085 115086 115087 115088 115089 151080 220020 220021 228480 228481 228482 228483 228720 231240 231241 231242 317160 495540 505680 505681 517980 517981 517982 517983 517984 517985 557280 557281 557282 580320 580321 580322 580323 580324 583260 599340 599341 599342 599343 599344 599345 611460 657300] INFO 2025-06-26 14:31:50,572 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:31:50,578 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 14:31:50,578 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2008.318.01 ERROR 2025-06-26 14:31:50,578 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2008.318.01 INFO 2025-06-26 14:31:50,591 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_cal.nc INFO 2025-06-26 14:31:52,057 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 14:31:52,063 process.py align():251 [1] Alignment steps for 2008.318.01 INFO 2025-06-26 14:31:52,089 align.py process_cal():139 [1] Processing dorado_2008.318.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2008.318.01 INFO 2025-06-26 14:31:52,109 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:31:52,112 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:31:52,155 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:31:52,159 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:31:52,202 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:31:52,206 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:31:52,230 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:31:52,230 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:31:52,248 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:31:52,252 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:31:52,296 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,300 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,338 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,341 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,379 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,382 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,419 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,423 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,462 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,466 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,506 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,543 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,546 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,583 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,586 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,623 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,627 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,663 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,667 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,705 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,709 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,745 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,748 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,785 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,788 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,825 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,829 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,867 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,870 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,908 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,911 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,949 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,952 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:52,990 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:52,994 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:53,033 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:53,036 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:53,074 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2008.318.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:31:53,078 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:31:53,126 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:31:53,160 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:31:53,192 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 14:31:53,227 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:31:53,262 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.07 INFO 2025-06-26 14:31:53,278 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_align.nc INFO 2025-06-26 14:31:53,342 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 14:31:53,344 process.py resample():273 [1] Resampling steps for 2008.318.01 INFO 2025-06-26 14:31:53,345 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:31:53,369 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_align.nc mission netCDF file INFO 2025-06-26 14:31:53,375 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_align.nc mission netCDF file INFO 2025-06-26 14:31:53,376 resample.py get_mission_start_end():1145 [1] navigation: 2008-11-13T15:44:42.189295104 to 2008-11-13T18:55:27.665226496 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 14:31:53,377 resample.py get_mission_start_end():1145 [1] hs2 : 2008-11-13T15:44:15.161146624 to 2008-11-13T18:55:27.645227776 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 14:31:53,379 resample.py get_mission_start_end():1145 [1] ctd1 : 2008-11-13T15:44:37.199636992 to 2008-11-13T18:55:27.705223680 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:31:53,380 resample.py get_mission_start_end():1145 [1] ctd2 : 2008-11-13T15:44:37.189637632 to 2008-11-13T18:55:27.685224960 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 14:31:53,382 resample.py get_mission_start_end():1145 [1] isus : 2008-11-13T15:45:31.575911936 to 2008-11-13T18:55:27.465240064 (0 days 00:00:00.239983616 before mission_end) INFO 2025-06-26 14:31:53,383 resample.py get_mission_start_end():1145 [1] biolume : 2008-11-13T15:44:09.201520640 to 2008-11-13T18:55:26.825249792 (0 days 00:00:00.879973888 before mission_end) INFO 2025-06-26 14:31:53,384 resample.py get_mission_start_end():1145 [1] tailcone : 2008-11-13T15:44:14.581186560 to 2008-11-13T18:55:27.575232512 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 14:31:53,385 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_align.nc mission netCDF file INFO 2025-06-26 14:31:53,385 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,522 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,548 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,574 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,600 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,623 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,646 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,668 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,690 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,710 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,730 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,750 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,770 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,789 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,809 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,828 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,848 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,870 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,890 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,912 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,932 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,953 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,974 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,986 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:53,998 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:54,010 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:54,022 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:54,035 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:31:54,191 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_1S.nc INFO 2025-06-26 14:31:56,001 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 14:31:58,153 create_products.py gulper_odv():522 [1] Wrote 2 Gulper data lines to /data/auv_data/dorado/missionodvs/2008.318.01/dorado_2008.318.01_1S_Gulper.txt INFO 2025-06-26 14:31:58,153 process.py archive():337 [1] Archiving steps for 2008.318.01 INFO 2025-06-26 14:31:58,153 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01, BASE_PATH = /data/auv_data INFO 2025-06-26 14:31:58,153 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01 files to /Volumes/AUVCTD/surveys/2008/netcdf INFO 2025-06-26 14:31:58,155 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.318.01_1S.nc INFO 2025-06-26 14:31:58,169 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_1S.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:31:58,170 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.318.01_cal.nc INFO 2025-06-26 14:31:58,219 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_cal.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:31:58,220 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2008/netcdf/dorado_2008.318.01_align.nc INFO 2025-06-26 14:31:58,263 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_align.nc /Volumes/AUVCTD/surveys/2008/netcdf done. INFO 2025-06-26 14:31:58,280 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,295 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,300 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,314 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,353 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,359 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,376 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,384 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,418 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,424 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2008/2008318/2008.318.01 done. INFO 2025-06-26 14:31:58,424 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:31:58,426 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2008/odv/dorado_2008.318.01_1S_Gulper.txt INFO 2025-06-26 14:31:58,430 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2008.318.01/dorado_2008.318.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2008/odv done. INFO 2025-06-26 14:31:58,430 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2008.318.01/dorado_2008.318.01_processing.log /Volumes/AUVCTD/surveys/2008/netcdf