INFO 2025-06-26 20:37:34,453 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:37:34,453 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB September 2014 with rhodamine sensor on ctdDriver2, channel 1 - ctdToUse = ctd1 INFO 2025-06-26 20:37:34,453 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.281.08 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:37:34,453 process.py download_process():165 [1] Download and processing steps for 2014.281.08 INFO 2025-06-26 20:37:34,454 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014281/2014.281.08 INFO 2025-06-26 20:37:34,454 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014281/2014.281.08 to /data/auv_data/dorado/missionlogs/2014.281.08 INFO 2025-06-26 20:37:36,041 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.281.08 INFO 2025-06-26 20:37:36,041 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/ctdDriver.log (1489446 bytes) INFO 2025-06-26 20:37:36,204 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/ctdDriver2.log (1489347 bytes) INFO 2025-06-26 20:37:36,335 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/gps.log (47372 bytes) INFO 2025-06-26 20:37:36,349 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/hydroscatlog.log (1307818 bytes) INFO 2025-06-26 20:37:36,594 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/navigation.log (5543010 bytes) INFO 2025-06-26 20:37:37,196 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/isuslog.log (95253 bytes) INFO 2025-06-26 20:37:37,211 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/parosci.log (1836278 bytes) INFO 2025-06-26 20:37:37,416 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/tailCone.log (933931 bytes) INFO 2025-06-26 20:37:37,563 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/biolume.log (1090982 bytes) INFO 2025-06-26 20:37:37,706 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:37:37,775 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.73 seconds INFO 2025-06-26 20:37:37,775 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.281.08/lopc.bin (12099522 bytes) INFO 2025-06-26 20:37:37,775 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:37:37 2025 INFO 2025-06-26 20:37:37,775 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.281.08/parosci.nc INFO 2025-06-26 20:37:37,775 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:37:37,775 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.281.08/parosci.nc INFO 2025-06-26 20:37:37,778 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1412803933.1, sensor_off_time = 1412807827.8 INFO 2025-06-26 20:37:37,778 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 3894 seconds. Expecting to read 7788 L frames from the lopc.bin file. INFO 2025-06-26 20:37:37,778 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 7788 records from the lopc.bin file. INFO 2025-06-26 20:37:37,850 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-10-08 21:32:13 Z and endTime = 2014-10-08 22:37:07 Z with 7788 records expected to be read from lopc.bin INFO 2025-06-26 20:37:37,850 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.281.08/lopc.bin INFO 2025-06-26 20:37:37,850 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.281.08/lopc.nc INFO 2025-06-26 20:37:37,851 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.281.08/lopc.nc INFO 2025-06-26 20:37:37,851 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.281.08 INFO 2025-06-26 20:37:37,852 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:37:37,857 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0107404 WARNING 2025-06-26 20:37:37,857 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:37:38,053 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:37:38,053 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:37:38,053 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:37:38,959 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:37:38,960 process.py calibrate():227 [1] Calibration steps for 2014.281.08 INFO 2025-06-26 20:37:39,059 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:37:39,061 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:37:39,540 calibrate.py _nudge_pos():1806 [1] 86: 0.010 -0.0000031 -0.0000220 15 0.05 -9.825 -87.504 2014-10-08T21:33:41.736989184 INFO 2025-06-26 20:37:39,940 calibrate.py _nudge_pos():1806 [1] 119: 0.010 -0.0007566 -0.0008923 3280 10.93 -10.263 -15.127 2014-10-08T21:45:09.729858304 INFO 2025-06-26 20:37:40,425 calibrate.py _nudge_pos():1806 [1] 160: 0.200 0.0000421 -0.0000018 24 0.08 81.442 -4.271 2014-10-08T21:45:54.536788992 INFO 2025-06-26 20:37:40,481 calibrate.py _nudge_pos():1806 [1] 165: 0.010 -0.0000241 0.0000062 15 0.05 -76.532 24.704 2014-10-08T21:46:01.736295680 INFO 2025-06-26 20:37:40,532 calibrate.py _nudge_pos():1806 [1] 170: 0.200 0.0003930 -0.0000424 1284 4.28 13.625 -1.837 2014-10-08T21:50:22.538429696 INFO 2025-06-26 20:37:40,993 calibrate.py _nudge_pos():1806 [1] 215: 0.010 0.0000138 0.0000503 30 0.10 21.145 96.476 2014-10-08T21:51:12.734990848 INFO 2025-06-26 20:37:41,230 calibrate.py _nudge_pos():1806 [1] 240: 0.200 -0.0004788 -0.0002299 1754 5.84 -12.148 -7.291 2014-10-08T21:57:27.539314944 INFO 2025-06-26 20:37:42,042 calibrate.py _nudge_pos():1806 [1] 323: 0.010 0.0003511 0.0000346 1330 4.43 11.751 1.448 2014-10-08T22:03:15.735461888 INFO 2025-06-26 20:37:42,339 calibrate.py _nudge_pos():1806 [1] 352: 0.010 -0.0000006 0.0000029 25 0.08 -1.118 6.647 2014-10-08T22:03:48.733201408 INFO 2025-06-26 20:37:42,694 calibrate.py _nudge_pos():1806 [1] 375: 0.010 -0.0000127 0.0000012 60 0.20 -9.580 1.134 2014-10-08T22:04:22.730872576 INFO 2025-06-26 20:37:42,742 calibrate.py _nudge_pos():1806 [1] 378: 0.010 -0.0003799 -0.0002126 1875 6.25 -9.018 -6.305 2014-10-08T22:10:39.735045888 INFO 2025-06-26 20:37:43,594 calibrate.py _nudge_pos():1806 [1] 455: 0.010 0.0000006 -0.0000217 15 0.05 1.882 -86.278 2014-10-08T22:11:58.739633920 INFO 2025-06-26 20:37:43,653 calibrate.py _nudge_pos():1806 [1] 459: 0.010 0.0002611 0.0000393 1265 4.21 9.189 1.730 2014-10-08T22:16:15.732028416 INFO 2025-06-26 20:37:44,448 calibrate.py _nudge_pos():1806 [1] 520: 0.200 -0.0002533 -0.0002346 2149 7.16 -5.244 -6.071 2014-10-08T22:24:27.538337536 INFO 2025-06-26 20:37:44,941 calibrate.py _nudge_pos():1806 [1] 569: 0.010 0.0003497 0.0000409 1470 4.90 10.590 1.546 2014-10-08T22:30:09.734895360 INFO 2025-06-26 20:37:45,352 calibrate.py _nudge_pos():1806 [1] 611: 0.010 -0.0004874 -0.0002809 1715 5.71 -12.648 -9.111 2014-10-08T22:36:33.738589440 INFO 2025-06-26 20:37:45,748 calibrate.py _nudge_pos():1862 [1] 600: - - - 0 0.00 - - INFO 2025-06-26 20:37:45,748 calibrate.py _nudge_pos():1868 [1] Points in final series = 19148 INFO 2025-06-26 20:37:45,831 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 3 of 15557 INFO 2025-06-26 20:37:45,955 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:46,122 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:46,283 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:46,285 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.281.08/ctd1.nc INFO 2025-06-26 20:37:46,286 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:37:46,287 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:37:46,287 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:37:46,461 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:46,581 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:46,583 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.281.08/ctd2.nc INFO 2025-06-26 20:37:46,584 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:37:46,585 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:37:46,585 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:37:46,597 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:37:46,856 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [600 601 602] INFO 2025-06-26 20:37:46,921 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:37:51,116 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.281.08 ERROR 2025-06-26 20:37:51,116 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.281.08 INFO 2025-06-26 20:37:51,135 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_cal.nc INFO 2025-06-26 20:37:51,205 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 20:37:51,212 process.py align():251 [1] Alignment steps for 2014.281.08 INFO 2025-06-26 20:37:51,244 align.py process_cal():139 [1] Processing dorado_2014.281.08_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.281.08 INFO 2025-06-26 20:37:51,258 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:51,261 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:51,287 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:51,290 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:51,316 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:51,319 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:51,331 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:37:51,332 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:37:51,341 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:51,344 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:51,366 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,369 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,390 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,393 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,413 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,416 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,442 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,446 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,473 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,477 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,497 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,500 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,520 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,522 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,543 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,546 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,566 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,569 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,589 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,591 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,611 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,614 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,634 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,637 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,657 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,660 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,681 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,683 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,704 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,707 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,727 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,730 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,750 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,753 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,774 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,777 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,797 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,800 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,820 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,823 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,844 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,847 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,879 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.281.08_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:51,883 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:51,924 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:37:51,959 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:37:51,994 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:37:52,031 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:37:52,070 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:37:52,114 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:37:52,281 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:52,300 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_align.nc INFO 2025-06-26 20:37:52,388 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 20:37:52,391 process.py resample():273 [1] Resampling steps for 2014.281.08 INFO 2025-06-26 20:37:52,392 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:37:52,430 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_align.nc mission netCDF file INFO 2025-06-26 20:37:52,438 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_align.nc mission netCDF file INFO 2025-06-26 20:37:52,440 resample.py get_mission_start_end():1145 [1] navigation: 2014-10-08T21:33:00.349824512 to 2014-10-08T22:37:07.736260352 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 20:37:52,442 resample.py get_mission_start_end():1145 [1] hs2 : 2014-10-08T21:32:17.422765312 to 2014-10-08T22:37:07.786257152 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:37:52,444 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-10-08T21:32:30.991835648 to 2014-10-08T22:37:07.646266624 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 20:37:52,446 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-10-08T21:32:31.321812992 to 2014-10-08T22:37:07.726261248 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:37:52,448 resample.py get_mission_start_end():1145 [1] isus : 2014-10-08T21:33:28.947865344 to 2014-10-08T22:37:07.536274176 (0 days 00:00:00.249982976 before mission_end) INFO 2025-06-26 20:37:52,449 resample.py get_mission_start_end():1145 [1] biolume : 2014-10-08T21:32:11.283151360 to 2014-10-08T22:37:06.436315392 (0 days 00:00:01.349941760 before mission_end) INFO 2025-06-26 20:37:52,451 resample.py get_mission_start_end():1145 [1] tailcone : 2014-10-08T21:32:18.762673408 to 2014-10-08T22:37:07.746259712 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 20:37:52,451 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_align.nc mission netCDF file INFO 2025-06-26 20:37:52,452 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,543 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,562 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,582 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,601 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,620 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,637 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,654 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,671 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,688 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,705 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,721 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,735 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,747 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,759 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,771 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,783 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,796 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,816 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,836 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,854 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,869 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,887 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,905 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,924 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,940 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,956 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,971 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,984 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:52,996 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:53,002 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:37:53,002 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:37:53,182 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:37:53,222 resample.py add_biolume_proxies():633 [1] Zero flow values found: 3896 of 3896 - replaced with 350 ml/s INFO 2025-06-26 20:37:53,222 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:37:53,246 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:37:53,258 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:37:53,271 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:37:53,272 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:37:53,301 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:53,524 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_1S.nc INFO 2025-06-26 20:37:55,011 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:37:55,612 create_products.py gulper_odv():522 [1] Wrote 3 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.281.08/dorado_2014.281.08_1S_Gulper.txt INFO 2025-06-26 20:37:55,613 process.py archive():337 [1] Archiving steps for 2014.281.08 INFO 2025-06-26 20:37:55,613 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08, BASE_PATH = /data/auv_data INFO 2025-06-26 20:37:55,613 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:37:55,615 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.281.08_1S.nc INFO 2025-06-26 20:37:55,624 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:37:55,624 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.281.08_cal.nc INFO 2025-06-26 20:37:55,657 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:37:55,659 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.281.08_align.nc INFO 2025-06-26 20:37:55,701 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:37:55,713 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,723 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,728 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,736 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,756 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,762 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,773 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,782 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,797 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,802 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014281/2014.281.08 done. INFO 2025-06-26 20:37:55,802 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:37:55,803 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.281.08_1S_Gulper.txt INFO 2025-06-26 20:37:55,808 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.281.08/dorado_2014.281.08_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:37:55,808 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.281.08/dorado_2014.281.08_processing.log /Volumes/AUVCTD/surveys/2014/netcdf