INFO 2025-06-26 20:36:01,240 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 20:36:01,240 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 20:36:01,240 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.280.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:36:01,240 process.py download_process():165 [1] Download and processing steps for 2014.280.01 INFO 2025-06-26 20:36:01,240 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014280/2014.280.01 INFO 2025-06-26 20:36:01,241 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014280/2014.280.01 to /data/auv_data/dorado/missionlogs/2014.280.01 INFO 2025-06-26 20:36:06,353 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.280.01 INFO 2025-06-26 20:36:06,354 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/ctdDriver.log (9117702 bytes) INFO 2025-06-26 20:36:07,024 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/ctdDriver2.log (9117795 bytes) INFO 2025-06-26 20:36:07,728 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/gps.log (215996 bytes) INFO 2025-06-26 20:36:07,758 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/hydroscatlog.log (7981114 bytes) INFO 2025-06-26 20:36:08,590 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/navigation.log (34148898 bytes) INFO 2025-06-26 20:36:11,063 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/isuslog.log (589813 bytes) INFO 2025-06-26 20:36:11,135 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/parosci.log (11191238 bytes) INFO 2025-06-26 20:36:12,247 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/tailCone.log (5702779 bytes) INFO 2025-06-26 20:36:13,335 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/biolume.log (6638354 bytes) INFO 2025-06-26 20:36:14,005 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:36:14,341 logs2netcdfs.py download_process_logs():807 [1] Time to process: 7.99 seconds INFO 2025-06-26 20:36:14,342 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.280.01/lopc.bin (43902283 bytes) INFO 2025-06-26 20:36:14,342 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:36:14 2025 INFO 2025-06-26 20:36:14,342 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.280.01/parosci.nc INFO 2025-06-26 20:36:14,342 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:36:14,342 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.280.01/parosci.nc INFO 2025-06-26 20:36:14,347 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1412699576.9, sensor_off_time = 1412723336.3 INFO 2025-06-26 20:36:14,347 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 23759 seconds. Expecting to read 47518 L frames from the lopc.bin file. INFO 2025-06-26 20:36:14,347 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 47518 records from the lopc.bin file. INFO 2025-06-26 20:36:14,718 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-10-07 16:32:56 Z and endTime = 2014-10-07 23:08:56 Z with 47518 records expected to be read from lopc.bin INFO 2025-06-26 20:36:14,718 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.280.01/lopc.bin INFO 2025-06-26 20:36:14,718 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.280.01/lopc.nc INFO 2025-06-26 20:36:14,718 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.280.01/lopc.nc INFO 2025-06-26 20:36:14,719 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.280.01 INFO 2025-06-26 20:36:14,719 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:36:14,880 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:36:14,880 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:36:14,880 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:36:21,514 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:36:21,515 process.py calibrate():227 [1] Calibration steps for 2014.280.01 INFO 2025-06-26 20:36:21,751 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 20:36:21,754 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:36:22,624 calibrate.py _nudge_pos():1806 [1] 114: 0.020 -0.0000229 0.0000128 20 0.06 -53.585 37.317 2014-10-07T16:34:52.317067264 INFO 2025-06-26 20:36:22,658 calibrate.py _nudge_pos():1806 [1] 116: 0.020 -0.0001473 0.0018886 3170 10.56 -2.071 33.131 2014-10-07T16:45:27.313566976 INFO 2025-06-26 20:36:24,529 calibrate.py _nudge_pos():1806 [1] 258: 0.030 0.0004355 0.0075716 13605 45.35 1.426 30.940 2014-10-07T17:33:09.317506048 INFO 2025-06-26 20:36:25,757 calibrate.py _nudge_pos():1806 [1] 367: 0.030 0.0038080 0.0071352 16260 54.20 10.441 24.396 2014-10-07T18:29:09.317330432 INFO 2025-06-26 20:36:26,590 calibrate.py _nudge_pos():1806 [1] 439: 0.040 0.0002357 0.0003657 545 1.81 19.312 37.373 2014-10-07T18:32:09.314999808 INFO 2025-06-26 20:36:27,534 calibrate.py _nudge_pos():1806 [1] 517: 0.040 -0.0004561 0.0026388 4655 15.51 -4.369 31.519 2014-10-07T18:48:57.315946752 INFO 2025-06-26 20:36:28,521 calibrate.py _nudge_pos():1806 [1] 594: 0.050 -0.0001487 0.0068538 13775 45.91 -0.481 27.661 2014-10-07T19:36:09.311941888 INFO 2025-06-26 20:36:29,747 calibrate.py _nudge_pos():1806 [1] 708: 0.060 -0.0032813 0.0063522 10805 36.01 -13.528 32.684 2014-10-07T20:14:03.316161792 INFO 2025-06-26 20:36:31,702 calibrate.py _nudge_pos():1806 [1] 841: 0.050 0.0000534 -0.0000291 25 0.08 99.082 -67.385 2014-10-07T20:16:20.316776704 INFO 2025-06-26 20:36:31,878 calibrate.py _nudge_pos():1806 [1] 855: 0.060 -0.0000812 0.0001172 260 0.86 -13.966 25.166 2014-10-07T20:17:25.312324352 INFO 2025-06-26 20:36:32,606 calibrate.py _nudge_pos():1806 [1] 909: 0.050 0.0000136 -0.0000152 20 0.06 31.859 -44.383 2014-10-07T20:18:22.318418944 INFO 2025-06-26 20:36:32,717 calibrate.py _nudge_pos():1806 [1] 920: 0.060 0.0000117 0.0000068 15 0.05 37.275 26.893 2014-10-07T20:18:35.317528576 INFO 2025-06-26 20:36:32,788 calibrate.py _nudge_pos():1806 [1] 927: 0.060 -0.0040990 0.0056538 6770 22.56 -26.973 46.432 2014-10-07T20:41:15.314362624 INFO 2025-06-26 20:36:33,284 calibrate.py _nudge_pos():1806 [1] 976: 0.050 -0.0000616 0.0000776 80 0.26 -34.724 54.625 2014-10-07T20:42:19.319977728 INFO 2025-06-26 20:36:34,476 calibrate.py _nudge_pos():1806 [1] 1086: 0.070 -0.0004866 0.0102480 16055 53.51 -1.351 35.486 2014-10-07T21:37:39.312542720 INFO 2025-06-26 20:36:35,939 calibrate.py _nudge_pos():1806 [1] 1196: 0.080 0.0026681 0.0114766 17600 58.66 6.758 36.251 2014-10-07T22:38:09.313870336 INFO 2025-06-26 20:36:39,732 calibrate.py _nudge_pos():1806 [1] 1501: 0.080 0.0000167 0.0000019 15 0.05 53.273 7.361 2014-10-07T22:43:18.312702720 INFO 2025-06-26 20:36:40,875 calibrate.py _nudge_pos():1806 [1] 1594: 0.080 0.0000081 0.0000162 30 0.10 12.512 31.018 2014-10-07T22:44:56.315988992 INFO 2025-06-26 20:36:40,932 calibrate.py _nudge_pos():1806 [1] 1599: 0.080 -0.0000104 -0.0000231 20 0.06 -24.507 -67.505 2014-10-07T22:45:04.315440896 INFO 2025-06-26 20:36:42,039 calibrate.py _nudge_pos():1806 [1] 1697: 0.080 0.0000386 0.0000180 15 0.05 122.982 71.404 2014-10-07T22:46:45.318521856 INFO 2025-06-26 20:36:45,371 calibrate.py _nudge_pos():1806 [1] 1944: 0.070 0.0000158 0.0000246 55 0.18 13.024 25.298 2014-10-07T22:51:03.320847616 INFO 2025-06-26 20:36:46,113 calibrate.py _nudge_pos():1806 [1] 2006: 0.080 0.0000434 -0.0000185 40 0.13 49.571 -26.394 2014-10-07T22:52:13.316052480 INFO 2025-06-26 20:36:46,167 calibrate.py _nudge_pos():1806 [1] 2011: 0.080 0.0000078 0.0000358 20 0.06 18.227 104.833 2014-10-07T22:52:21.315504384 INFO 2025-06-26 20:36:47,508 calibrate.py _nudge_pos():1806 [1] 2130: 0.080 0.0000632 0.0000472 30 0.10 97.128 90.395 2014-10-07T22:54:25.317009664 INFO 2025-06-26 20:36:49,915 calibrate.py _nudge_pos():1806 [1] 2335: 0.080 0.0000208 0.0000375 25 0.08 38.583 86.805 2014-10-07T22:57:54.312692736 INFO 2025-06-26 20:36:54,659 calibrate.py _nudge_pos():1806 [1] 2796: 0.070 0.0001814 -0.0001491 35 0.11 237.893 -243.743 2014-10-07T23:05:44.320494848 INFO 2025-06-26 20:36:56,572 calibrate.py _nudge_pos():1862 [1] 2940: - - - 5 0.01 - - INFO 2025-06-26 20:36:56,573 calibrate.py _nudge_pos():1868 [1] Points in final series = 118564 INFO 2025-06-26 20:36:56,911 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 21 of 95001 INFO 2025-06-26 20:36:57,662 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:36:58,560 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:36:59,273 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:36:59,275 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.280.01/ctd1.nc INFO 2025-06-26 20:36:59,276 calibrate.py _range_qc_combined_nc():898 [1] Setting 3 ctd1_salinity values to NaN INFO 2025-06-26 20:36:59,277 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 20:36:59,277 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:37:00,202 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:00,920 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:37:00,922 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.280.01/ctd2.nc INFO 2025-06-26 20:37:00,923 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 20:37:00,924 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 20:37:00,924 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:37:00,963 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:37:02,234 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:37:02,272 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.280.01 ERROR 2025-06-26 20:37:02,272 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.280.01 INFO 2025-06-26 20:37:02,366 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_cal.nc INFO 2025-06-26 20:37:02,523 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 20:37:02,529 process.py align():251 [1] Alignment steps for 2014.280.01 INFO 2025-06-26 20:37:02,570 align.py process_cal():139 [1] Processing dorado_2014.280.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.280.01 INFO 2025-06-26 20:37:02,604 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:02,608 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:02,687 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:02,692 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:02,771 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:02,777 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:02,823 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:37:02,824 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:37:02,853 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:37:02,859 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:02,936 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:02,941 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,008 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,013 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,081 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,086 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,153 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,158 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,226 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,230 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,297 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,302 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,370 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,375 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,444 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,449 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,519 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,524 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,592 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,598 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,666 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,671 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,740 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,744 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,813 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,818 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,887 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,891 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:03,961 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:03,966 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,033 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,038 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,109 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,114 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,184 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,190 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,262 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,267 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,338 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,344 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,414 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,419 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,487 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.280.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:37:04,492 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:37:04,580 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:37:04,639 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:37:04,698 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:37:04,760 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:37:04,824 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:37:04,932 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:37:05,542 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:37:05,598 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_align.nc INFO 2025-06-26 20:37:05,762 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 20:37:05,764 process.py resample():273 [1] Resampling steps for 2014.280.01 INFO 2025-06-26 20:37:05,765 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:37:05,804 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_align.nc mission netCDF file INFO 2025-06-26 20:37:05,810 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_align.nc mission netCDF file INFO 2025-06-26 20:37:05,812 resample.py get_mission_start_end():1145 [1] navigation: 2014-10-07T16:33:43.731765504 to 2014-10-07T23:08:56.317341952 (0 days 00:00:00.029998080 before mission_end) INFO 2025-06-26 20:37:05,814 resample.py get_mission_start_end():1145 [1] hs2 : 2014-10-07T16:33:00.814705664 to 2014-10-07T23:08:56.347340032 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:37:05,815 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-10-07T16:33:14.663756800 to 2014-10-07T23:08:56.167352320 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 20:37:05,817 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-10-07T16:33:14.393775104 to 2014-10-07T23:08:56.147353856 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 20:37:05,818 resample.py get_mission_start_end():1145 [1] isus : 2014-10-07T16:34:10.699918080 to 2014-10-07T23:08:56.157353216 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 20:37:05,820 resample.py get_mission_start_end():1145 [1] biolume : 2014-10-07T16:32:54.645093888 to 2014-10-07T23:08:55.327375616 (0 days 00:00:01.019964416 before mission_end) INFO 2025-06-26 20:37:05,822 resample.py get_mission_start_end():1145 [1] tailcone : 2014-10-07T16:32:56.984967936 to 2014-10-07T23:08:56.167352320 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 20:37:05,822 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_align.nc mission netCDF file INFO 2025-06-26 20:37:05,823 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,090 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,135 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,179 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,224 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,263 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,302 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,340 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,377 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,412 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,448 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,498 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,545 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,580 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,616 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,651 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,693 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,729 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,768 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,812 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,850 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,891 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,932 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:06,972 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,011 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,030 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,048 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,064 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,081 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,097 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:07,104 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:37:07,104 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:37:07,951 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:37:08,189 resample.py add_biolume_proxies():633 [1] Zero flow values found: 23762 of 23762 - replaced with 350 ml/s INFO 2025-06-26 20:37:08,190 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:37:08,299 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:37:08,357 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:37:08,413 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:37:08,413 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:37:08,478 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:37:08,788 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_1S.nc INFO 2025-06-26 20:37:11,296 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:37:33,599 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.280.01/dorado_2014.280.01_1S_Gulper.txt INFO 2025-06-26 20:37:33,600 process.py archive():337 [1] Archiving steps for 2014.280.01 INFO 2025-06-26 20:37:33,600 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:37:33,602 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:37:33,603 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.280.01_1S.nc INFO 2025-06-26 20:37:33,630 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:37:33,631 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.280.01_cal.nc INFO 2025-06-26 20:37:33,800 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:37:33,801 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.280.01_align.nc INFO 2025-06-26 20:37:34,027 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:37:34,060 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,089 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,095 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,123 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,232 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,240 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,276 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,302 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,375 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,385 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014280/2014.280.01 done. INFO 2025-06-26 20:37:34,385 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:37:34,387 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.280.01_1S_Gulper.txt INFO 2025-06-26 20:37:34,392 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.280.01/dorado_2014.280.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:37:34,392 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.280.01/dorado_2014.280.01_processing.log /Volumes/AUVCTD/surveys/2014/netcdf