INFO 2025-06-26 20:40:50,291 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 20:40:50,292 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2014 Northern Monterey Bay gulper missions - ctdToUse = ctd1 INFO 2025-06-26 20:40:50,292 process.py process_mission():449 [1] Processing SIMZ October 2014 mission 2014.290.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:40:50,292 process.py download_process():165 [1] Download and processing steps for 2014.290.00 INFO 2025-06-26 20:40:50,292 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014290/2014.290.00 INFO 2025-06-26 20:40:50,292 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014290/2014.290.00 to /data/auv_data/dorado/missionlogs/2014.290.00 INFO 2025-06-26 20:40:53,790 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.290.00 INFO 2025-06-26 20:40:53,791 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/ctdDriver.log (7389702 bytes) INFO 2025-06-26 20:40:54,438 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/ctdDriver2.log (7389599 bytes) INFO 2025-06-26 20:40:55,378 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/gps.log (174020 bytes) INFO 2025-06-26 20:40:55,426 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/hydroscatlog.log (6468778 bytes) INFO 2025-06-26 20:40:56,298 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/navigation.log (27682146 bytes) INFO 2025-06-26 20:40:58,906 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/isuslog.log (477621 bytes) INFO 2025-06-26 20:40:58,976 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/parosci.log (9090662 bytes) INFO 2025-06-26 20:40:59,763 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/tailCone.log (4624795 bytes) INFO 2025-06-26 20:41:00,384 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/biolume.log (5384210 bytes) INFO 2025-06-26 20:41:00,926 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:41:01,208 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.42 seconds INFO 2025-06-26 20:41:01,209 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.290.00/lopc.bin (19483302 bytes) INFO 2025-06-26 20:41:01,209 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:41:01 2025 INFO 2025-06-26 20:41:01,209 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.290.00/parosci.nc INFO 2025-06-26 20:41:01,209 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:41:01,209 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.290.00/parosci.nc INFO 2025-06-26 20:41:01,212 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1413560234.9, sensor_off_time = 1413579500.6 INFO 2025-06-26 20:41:01,213 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 19265 seconds. Expecting to read 38530 L frames from the lopc.bin file. INFO 2025-06-26 20:41:01,213 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 38530 records from the lopc.bin file. INFO 2025-06-26 20:41:01,540 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-10-17 15:37:14 Z and endTime = 2014-10-17 20:58:20 Z with 38530 records expected to be read from lopc.bin INFO 2025-06-26 20:41:01,541 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.290.00/lopc.bin INFO 2025-06-26 20:41:01,541 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.290.00/lopc.nc INFO 2025-06-26 20:41:01,541 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.290.00/lopc.nc INFO 2025-06-26 20:41:01,542 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.290.00 INFO 2025-06-26 20:41:01,542 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:41:01,547 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:41:01,631 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:41:01,631 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:41:01,631 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 20:41:13,392 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 57162 23342 0 0 0 0 0 11.9 seconds, last L Frame: 38530 INFO 2025-06-26 20:41:17,807 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 1626 32455 0 0 0 0 0 4.4 seconds, last L Frame: 38530 ERROR 2025-06-26 20:41:20,327 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:41:20,329 process.py calibrate():227 [1] Calibration steps for 2014.290.00 INFO 2025-06-26 20:41:20,633 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 20:41:20,635 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:41:21,894 calibrate.py _nudge_pos():1806 [1] 147: 0.140 -0.0003924 0.0003753 2595 8.65 -6.720 8.043 2014-10-17T15:48:16.157548800 INFO 2025-06-26 20:41:23,081 calibrate.py _nudge_pos():1806 [1] 248: 0.140 0.0003281 0.0004081 8825 29.41 1.652 2.571 2014-10-17T16:19:22.159718912 INFO 2025-06-26 20:41:23,984 calibrate.py _nudge_pos():1806 [1] 320: 0.150 0.0004074 0.0006586 8375 27.91 2.162 4.372 2014-10-17T16:48:28.150110464 INFO 2025-06-26 20:41:25,019 calibrate.py _nudge_pos():1806 [1] 406: 0.160 0.0002275 0.0006129 6775 22.58 1.493 5.030 2014-10-17T17:12:28.151463680 INFO 2025-06-26 20:41:26,067 calibrate.py _nudge_pos():1806 [1] 492: 0.150 0.0001831 0.0001512 3445 11.48 2.363 2.441 2014-10-17T17:25:22.158440704 INFO 2025-06-26 20:41:28,478 calibrate.py _nudge_pos():1806 [1] 686: 0.160 -0.0027196 0.0009657 6085 20.28 -19.874 8.824 2014-10-17T17:48:52.151849216 INFO 2025-06-26 20:41:29,626 calibrate.py _nudge_pos():1806 [1] 796: 0.160 -0.0034531 0.0010046 7345 24.48 -20.909 7.605 2014-10-17T18:15:10.153748736 INFO 2025-06-26 20:41:32,609 calibrate.py _nudge_pos():1806 [1] 1045: 0.170 -0.0032519 0.0008205 7040 23.46 -20.547 6.480 2014-10-17T18:42:46.150305280 INFO 2025-06-26 20:41:33,475 calibrate.py _nudge_pos():1806 [1] 1127: 0.170 -0.0010718 -0.0004931 1755 5.85 -27.178 -15.627 2014-10-17T18:49:58.150711296 INFO 2025-06-26 20:41:34,721 calibrate.py _nudge_pos():1806 [1] 1223: 0.160 0.0008771 0.0001979 3515 11.71 11.103 3.131 2014-10-17T19:03:16.156044032 INFO 2025-06-26 20:41:37,841 calibrate.py _nudge_pos():1806 [1] 1475: 0.160 -0.0005077 0.0001692 3305 11.01 -6.834 2.846 2014-10-17T19:18:28.153568000 INFO 2025-06-26 20:41:37,974 calibrate.py _nudge_pos():1806 [1] 1483: 0.170 0.0000079 -0.0000467 220 0.73 1.596 -11.848 2014-10-17T19:19:19.150074368 INFO 2025-06-26 20:41:40,121 calibrate.py _nudge_pos():1806 [1] 1653: 0.170 -0.0008030 -0.0004753 4720 15.73 -7.568 -5.599 2014-10-17T19:37:52.153828608 INFO 2025-06-26 20:41:42,955 calibrate.py _nudge_pos():1806 [1] 1883: 0.170 -0.0011800 -0.0008860 5935 19.78 -8.842 -8.300 2014-10-17T20:01:28.156825856 INFO 2025-06-26 20:41:45,570 calibrate.py _nudge_pos():1806 [1] 2082: 0.180 -0.0011131 -0.0009423 6630 22.10 -7.465 -7.902 2014-10-17T20:26:52.152424704 INFO 2025-06-26 20:41:46,425 calibrate.py _nudge_pos():1806 [1] 2146: 0.180 -0.0004531 -0.0003179 5265 17.55 -3.826 -3.357 2014-10-17T20:45:28.155973376 INFO 2025-06-26 20:41:47,807 calibrate.py _nudge_pos():1806 [1] 2256: 0.180 0.0000010 -0.0004197 2575 8.58 0.018 -9.064 2014-10-17T20:55:52.153226496 INFO 2025-06-26 20:41:49,750 calibrate.py _nudge_pos():1862 [1] 2358: - - - 1 0.00 - - INFO 2025-06-26 20:41:49,750 calibrate.py _nudge_pos():1868 [1] Points in final series = 96109 INFO 2025-06-26 20:41:50,643 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:41:51,499 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:41:52,092 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:41:52,094 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.290.00/ctd1.nc INFO 2025-06-26 20:41:52,095 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:41:52,096 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 20:41:52,096 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:41:52,964 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:41:53,529 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:41:53,532 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.290.00/ctd2.nc INFO 2025-06-26 20:41:53,533 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:41:53,533 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 20:41:53,533 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:41:53,566 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:41:54,459 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 20:41:54,625 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:42:12,107 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.290.00 ERROR 2025-06-26 20:42:12,107 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.290.00 INFO 2025-06-26 20:42:12,184 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_cal.nc INFO 2025-06-26 20:42:12,325 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 20:42:12,332 process.py align():251 [1] Alignment steps for 2014.290.00 INFO 2025-06-26 20:42:12,376 align.py process_cal():139 [1] Processing dorado_2014.290.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.290.00 INFO 2025-06-26 20:42:12,410 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:42:12,415 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:42:12,484 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:42:12,490 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:42:12,594 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:42:12,603 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:42:12,648 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:42:12,648 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:42:12,674 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:42:12,679 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:42:12,744 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:12,749 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:12,805 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:12,809 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:12,867 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:12,871 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:12,928 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:12,932 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:12,990 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:12,995 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,051 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,055 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,114 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,118 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,173 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,178 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,234 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,239 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,294 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,299 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,355 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,360 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,419 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,424 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,484 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,488 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,546 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,550 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,609 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,614 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,670 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,675 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,733 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,738 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,794 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,799 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,857 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,862 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,919 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,924 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:13,983 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:13,987 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:14,045 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.290.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:42:14,049 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:42:14,121 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:42:14,171 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:42:14,221 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:42:14,274 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:42:14,328 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:42:14,414 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:42:14,901 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:42:14,947 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_align.nc INFO 2025-06-26 20:42:15,085 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 20:42:15,087 process.py resample():273 [1] Resampling steps for 2014.290.00 INFO 2025-06-26 20:42:15,088 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:42:15,123 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_align.nc mission netCDF file INFO 2025-06-26 20:42:15,129 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_align.nc mission netCDF file INFO 2025-06-26 20:42:15,130 resample.py get_mission_start_end():1145 [1] navigation: 2014-10-17T15:37:58.769842944 to 2014-10-17T20:58:20.553060608 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 20:42:15,132 resample.py get_mission_start_end():1145 [1] hs2 : 2014-10-17T15:37:21.452399360 to 2014-10-17T20:58:20.533061888 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:42:15,134 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-10-17T15:37:38.981198592 to 2014-10-17T20:58:20.533061888 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:42:15,135 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-10-17T15:37:39.021195776 to 2014-10-17T20:58:20.583058432 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 20:42:15,137 resample.py get_mission_start_end():1145 [1] isus : 2014-10-17T15:38:29.717722880 to 2014-10-17T20:58:20.593057792 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:42:15,138 resample.py get_mission_start_end():1145 [1] biolume : 2014-10-17T15:37:10.653104896 to 2014-10-17T20:58:19.673086720 (0 days 00:00:00.919971072 before mission_end) INFO 2025-06-26 20:42:15,140 resample.py get_mission_start_end():1145 [1] tailcone : 2014-10-17T15:37:12.802991872 to 2014-10-17T20:58:20.543061248 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 20:42:15,141 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_align.nc mission netCDF file INFO 2025-06-26 20:42:15,141 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,356 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,393 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,430 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,466 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,498 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,529 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,560 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,591 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,621 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,650 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,679 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,708 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,738 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,767 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,797 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,826 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,856 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,888 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,920 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,951 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:15,983 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,017 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,049 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,080 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,097 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,112 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,127 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,141 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,154 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:16,160 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:42:16,160 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:42:16,929 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:42:17,068 resample.py add_biolume_proxies():633 [1] Zero flow values found: 18231 of 19270 - replaced with 350 ml/s INFO 2025-06-26 20:42:17,068 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:42:17,139 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:42:17,169 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:42:17,195 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:42:17,195 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:42:17,235 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:42:17,460 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_1S.nc INFO 2025-06-26 20:42:19,389 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:42:41,090 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.290.00/dorado_2014.290.00_1S_Gulper.txt INFO 2025-06-26 20:42:41,090 process.py archive():337 [1] Archiving steps for 2014.290.00 INFO 2025-06-26 20:42:41,091 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:42:41,092 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:42:41,093 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.290.00_1S.nc INFO 2025-06-26 20:42:41,113 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:42:41,114 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.290.00_cal.nc INFO 2025-06-26 20:42:41,241 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:42:41,242 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.290.00_align.nc INFO 2025-06-26 20:42:41,423 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:42:41,447 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,468 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,473 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,494 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,567 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,573 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,600 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,619 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,672 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,713 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014290/2014.290.00 done. INFO 2025-06-26 20:42:41,714 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:42:41,715 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.290.00_1S_Gulper.txt INFO 2025-06-26 20:42:41,719 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.290.00/dorado_2014.290.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:42:41,720 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.290.00/dorado_2014.290.00_processing.log /Volumes/AUVCTD/surveys/2014/netcdf