INFO 2025-06-26 19:00:37,895 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 19:00:37,895 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX missions - Initial engineering test from Yanwu & Frederic - ctdToUse = ctd1 INFO 2025-06-26 19:00:37,895 process.py process_mission():449 [1] Processing AUVCTD mission 2012.143.07 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:00:37,895 process.py download_process():165 [1] Download and processing steps for 2012.143.07 INFO 2025-06-26 19:00:37,895 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2012/2012143/2012.143.07 INFO 2025-06-26 19:00:37,895 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2012/2012143/2012.143.07 to /data/auv_data/dorado/missionlogs/2012.143.07 INFO 2025-06-26 19:00:39,879 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2012.143.07 INFO 2025-06-26 19:00:39,880 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/ctdDriver.log (961926 bytes) INFO 2025-06-26 19:00:39,976 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/ctdDriver2.log (961727 bytes) INFO 2025-06-26 19:00:40,071 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/gps.log (39884 bytes) INFO 2025-06-26 19:00:40,089 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/hydroscatlog.log (848086 bytes) INFO 2025-06-26 19:00:40,197 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/navigation.log (3392518 bytes) INFO 2025-06-26 19:00:40,486 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/parosci.log (1029446 bytes) INFO 2025-06-26 19:00:40,600 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/tailCone.log (607387 bytes) INFO 2025-06-26 19:00:40,712 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/biolume.log (709854 bytes) INFO 2025-06-26 19:00:40,797 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:00:40,841 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.96 seconds INFO 2025-06-26 19:00:40,841 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2012.143.07/lopc.bin (5748000 bytes) INFO 2025-06-26 19:00:40,841 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:00:40 2025 INFO 2025-06-26 19:00:40,842 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2012.143.07/parosci.nc INFO 2025-06-26 19:00:40,842 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:00:40,842 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2012.143.07/parosci.nc INFO 2025-06-26 19:00:40,844 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1337706000.2, sensor_off_time = 1337708530.6 INFO 2025-06-26 19:00:40,844 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 2530 seconds. Expecting to read 5060 L frames from the lopc.bin file. INFO 2025-06-26 19:00:40,844 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 5060 records from the lopc.bin file. INFO 2025-06-26 19:00:40,875 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2012-05-22 17:00:00 Z and endTime = 2012-05-22 17:42:10 Z with 5060 records expected to be read from lopc.bin INFO 2025-06-26 19:00:40,876 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2012.143.07/lopc.bin INFO 2025-06-26 19:00:40,876 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2012.143.07/lopc.nc INFO 2025-06-26 19:00:40,876 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2012.143.07/lopc.nc INFO 2025-06-26 19:00:40,877 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2012.143.07 INFO 2025-06-26 19:00:40,877 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:00:40,880 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0177787 WARNING 2025-06-26 19:00:40,880 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:00:40,965 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:00:40,965 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:00:40,965 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:00:43,482 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:00:43,483 process.py calibrate():227 [1] Calibration steps for 2012.143.07 INFO 2025-06-26 19:00:43,572 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 19:00:43,574 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:00:44,718 calibrate.py _nudge_pos():1806 [1] 149: 0.040 -0.0001376 -0.0022099 2315 7.71 -2.643 -53.089 2012-05-22T17:10:10.442783232 INFO 2025-06-26 19:00:44,728 calibrate.py _nudge_pos():1806 [1] 150: 0.020 -0.0000192 -0.0000030 65 0.21 -13.309 -2.568 2012-05-22T17:10:23.451892224 INFO 2025-06-26 19:00:45,021 calibrate.py _nudge_pos():1806 [1] 181: 0.030 0.0000021 0.0000256 25 0.08 3.872 59.384 2012-05-22T17:10:58.449494528 INFO 2025-06-26 19:00:45,627 calibrate.py _nudge_pos():1806 [1] 246: 0.030 -0.0000047 0.0000368 20 0.06 -11.078 107.659 2012-05-22T17:12:06.444836608 INFO 2025-06-26 19:00:45,638 calibrate.py _nudge_pos():1806 [1] 247: 0.030 -0.0004289 -0.0023984 2570 8.56 -7.423 -51.899 2012-05-22T17:20:40.449624832 INFO 2025-06-26 19:00:45,839 calibrate.py _nudge_pos():1806 [1] 268: 0.030 0.0000420 -0.0000298 20 0.06 98.401 -87.114 2012-05-22T17:21:04.447980800 INFO 2025-06-26 19:00:46,564 calibrate.py _nudge_pos():1806 [1] 345: 0.030 -0.0000016 0.0000057 30 0.10 -2.377 10.936 2012-05-22T17:22:26.442363648 INFO 2025-06-26 19:00:46,604 calibrate.py _nudge_pos():1806 [1] 349: 0.020 -0.0009285 -0.0019564 2575 8.58 -16.037 -42.251 2012-05-22T17:31:04.446878208 INFO 2025-06-26 19:00:46,974 calibrate.py _nudge_pos():1806 [1] 388: 0.030 0.0001148 -0.0000803 20 0.06 268.535 -234.962 2012-05-22T17:31:46.444001280 INFO 2025-06-26 19:00:47,578 calibrate.py _nudge_pos():1806 [1] 452: 0.020 0.0000126 -0.0000008 15 0.05 39.985 -3.250 2012-05-22T17:32:52.449479424 INFO 2025-06-26 19:00:47,634 calibrate.py _nudge_pos():1806 [1] 458: 0.030 0.0000051 -0.0000066 20 0.06 11.957 -19.381 2012-05-22T17:33:01.448862976 INFO 2025-06-26 19:00:47,827 calibrate.py _nudge_pos():1806 [1] 478: 0.030 0.0000203 -0.0000207 15 0.05 64.519 -82.212 2012-05-22T17:33:23.447355904 INFO 2025-06-26 19:00:47,954 calibrate.py _nudge_pos():1806 [1] 491: 0.040 -0.0010524 -0.0014128 2300 7.66 -20.351 -34.162 2012-05-22T17:41:17.444884736 INFO 2025-06-26 19:00:48,012 calibrate.py _nudge_pos():1806 [1] 497: 0.030 0.0000146 0.0000120 20 0.06 34.180 34.991 2012-05-22T17:41:26.444268544 INFO 2025-06-26 19:00:48,441 calibrate.py _nudge_pos():1862 [1] 504: - - - 1 0.00 - - INFO 2025-06-26 19:00:48,441 calibrate.py _nudge_pos():1868 [1] Points in final series = 12464 WARNING 2025-06-26 19:00:48,462 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 19:00:48,576 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:00:48,694 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:48,776 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:48,778 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2012.143.07/ctd1.nc INFO 2025-06-26 19:00:48,779 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 19:00:48,779 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 19:00:48,779 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:00:48,889 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:48,971 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:00:48,973 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2012.143.07/ctd2.nc INFO 2025-06-26 19:00:48,974 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:00:48,974 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 19:00:48,974 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:00:48,975 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.143.07 INFO 2025-06-26 19:00:48,978 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:00:49,117 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:00:49,131 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2012.143.07 ERROR 2025-06-26 19:00:49,131 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2012.143.07 INFO 2025-06-26 19:00:49,145 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_cal.nc INFO 2025-06-26 19:00:49,206 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 19:00:49,213 process.py align():251 [1] Alignment steps for 2012.143.07 INFO 2025-06-26 19:00:49,245 align.py process_cal():139 [1] Processing dorado_2012.143.07_cal.nc from /data/auv_data/dorado/missionnetcdfs/2012.143.07 INFO 2025-06-26 19:00:49,254 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:49,256 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:49,275 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:49,278 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:49,295 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:49,298 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:49,309 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:00:49,309 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:00:49,317 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:00:49,320 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:49,339 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,341 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,358 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,361 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,378 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,380 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,397 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,400 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,418 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,421 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,440 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,442 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,462 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,466 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,483 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,486 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,504 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,520 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,523 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,539 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,542 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,558 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,561 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,577 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,579 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,595 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,598 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,616 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,619 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,636 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,639 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,657 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,660 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,678 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,681 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,700 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,702 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,720 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,722 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,740 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,743 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,760 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2012.143.07_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:00:49,762 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:00:49,784 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:00:49,803 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:00:49,825 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 19:00:49,907 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:00:49,922 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_align.nc INFO 2025-06-26 19:00:49,986 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 19:00:49,989 process.py resample():273 [1] Resampling steps for 2012.143.07 INFO 2025-06-26 19:00:49,990 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:00:50,023 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_align.nc mission netCDF file INFO 2025-06-26 19:00:50,030 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_align.nc mission netCDF file INFO 2025-06-26 19:00:50,032 resample.py get_mission_start_end():1145 [1] navigation: 2012-05-22T17:00:38.061993984 to 2012-05-22T17:42:10.651239936 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:00:50,034 resample.py get_mission_start_end():1145 [1] hs2 : 2012-05-22T17:00:08.484020224 to 2012-05-22T17:42:10.551246848 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 19:00:50,036 resample.py get_mission_start_end():1145 [1] ctd1 : 2012-05-22T17:00:27.512716800 to 2012-05-22T17:42:10.441254400 (0 days 00:00:00.209985536 before mission_end) INFO 2025-06-26 19:00:50,037 resample.py get_mission_start_end():1145 [1] ctd2 : 2012-05-22T17:00:27.862692864 to 2012-05-22T17:42:10.541247488 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 19:00:50,039 resample.py get_mission_start_end():1145 [1] biolume : 2012-05-22T16:59:59.304614656 to 2012-05-22T17:42:09.661273600 (0 days 00:00:00.989966336 before mission_end) INFO 2025-06-26 19:00:50,041 resample.py get_mission_start_end():1145 [1] tailcone : 2012-05-22T17:00:02.194451200 to 2012-05-22T17:42:10.581244672 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 19:00:50,041 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_align.nc mission netCDF file INFO 2025-06-26 19:00:50,042 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,103 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,117 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,130 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,142 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,155 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,167 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,179 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,192 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,204 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,217 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,230 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,242 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,255 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,267 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,279 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,291 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,301 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,315 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,327 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,339 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,351 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,363 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,375 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,387 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,395 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,403 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,407 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:00:50,407 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:00:50,489 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:00:50,510 resample.py add_biolume_proxies():633 [1] Zero flow values found: 1 of 2531 - replaced with 350 ml/s INFO 2025-06-26 19:00:50,510 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:00:50,520 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:00:50,526 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:00:50,534 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:00:50,534 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:00:50,552 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:00:50,675 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_1S.nc INFO 2025-06-26 19:00:52,115 create_products.py gulper_odv():401 [1] No gulper times found for 2012.143.07 INFO 2025-06-26 19:00:52,115 process.py archive():337 [1] Archiving steps for 2012.143.07 INFO 2025-06-26 19:00:52,115 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07, BASE_PATH = /data/auv_data INFO 2025-06-26 19:00:52,115 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07 files to /Volumes/AUVCTD/surveys/2012/netcdf INFO 2025-06-26 19:00:52,119 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.143.07_1S.nc INFO 2025-06-26 19:00:52,130 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_1S.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:52,131 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.143.07_cal.nc INFO 2025-06-26 19:00:52,154 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_cal.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:52,155 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2012/netcdf/dorado_2012.143.07_align.nc INFO 2025-06-26 19:00:52,191 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_align.nc /Volumes/AUVCTD/surveys/2012/netcdf done. INFO 2025-06-26 19:00:52,203 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,213 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,219 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/gps.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,228 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,243 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,252 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,262 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,280 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,287 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2012/2012143/2012.143.07 done. INFO 2025-06-26 19:00:52,288 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:00:52,288 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2012.143.07/dorado_2012.143.07_processing.log /Volumes/AUVCTD/surveys/2012/netcdf