INFO 2025-06-26 20:01:17,384 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 20:01:17,384 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Autonomy group's short missions in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:01:17,384 process.py process_mission():449 [1] Processing AUVCTD mission 2013.287.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:01:17,384 process.py download_process():165 [1] Download and processing steps for 2013.287.02 INFO 2025-06-26 20:01:17,384 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013287/2013.287.02 INFO 2025-06-26 20:01:17,384 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013287/2013.287.02 to /data/auv_data/dorado/missionlogs/2013.287.02 INFO 2025-06-26 20:01:21,289 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.287.02 INFO 2025-06-26 20:01:21,289 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/ctdDriver.log (4500774 bytes) INFO 2025-06-26 20:01:21,623 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/ctdDriver2.log (4500575 bytes) INFO 2025-06-26 20:01:21,942 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/gps.log (292388 bytes) INFO 2025-06-26 20:01:21,980 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/hydroscatlog.log (3944074 bytes) INFO 2025-06-26 20:01:22,385 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/navigation.log (15932262 bytes) INFO 2025-06-26 20:01:23,500 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/parosci.log (5545526 bytes) INFO 2025-06-26 20:01:23,963 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/tailCone.log (2819035 bytes) INFO 2025-06-26 20:01:24,311 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/biolume.log (3283178 bytes) INFO 2025-06-26 20:01:24,646 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:01:24,811 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.52 seconds INFO 2025-06-26 20:01:24,812 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.02/lopc.bin (31584431 bytes) INFO 2025-06-26 20:01:24,812 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:01:24 2025 INFO 2025-06-26 20:01:24,812 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.287.02/parosci.nc INFO 2025-06-26 20:01:24,812 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:01:24,812 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.287.02/parosci.nc INFO 2025-06-26 20:01:24,815 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381773122.2, sensor_off_time = 1381784866.0 INFO 2025-06-26 20:01:24,816 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11743 seconds. Expecting to read 23486 L frames from the lopc.bin file. INFO 2025-06-26 20:01:24,816 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 23486 records from the lopc.bin file. INFO 2025-06-26 20:01:24,955 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-14 17:52:02 Z and endTime = 2013-10-14 21:07:45 Z with 23486 records expected to be read from lopc.bin INFO 2025-06-26 20:01:24,955 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.287.02/lopc.bin INFO 2025-06-26 20:01:24,955 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.287.02/lopc.nc INFO 2025-06-26 20:01:24,955 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.287.02/lopc.nc INFO 2025-06-26 20:01:24,956 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.287.02 INFO 2025-06-26 20:01:24,956 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:01:24,959 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:01:25,002 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:01:25,003 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:01:25,003 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:01:25,553 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:01:25,554 process.py calibrate():227 [1] Calibration steps for 2013.287.02 INFO 2025-06-26 20:01:25,686 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 20:01:25,688 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:01:30,197 calibrate.py _nudge_pos():1806 [1] 520: 0.190 0.0006327 -0.0000489 3015 10.05 9.332 -0.901 2013-10-14T18:10:39.977879040 INFO 2025-06-26 20:01:32,282 calibrate.py _nudge_pos():1806 [1] 747: 0.190 0.0003270 0.0000769 3909 13.03 3.720 1.094 2013-10-14T18:27:27.978826240 INFO 2025-06-26 20:01:34,220 calibrate.py _nudge_pos():1806 [1] 957: 0.200 0.0000774 0.0000729 2614 8.71 1.317 1.551 2013-10-14T18:39:39.978680832 INFO 2025-06-26 20:01:35,801 calibrate.py _nudge_pos():1806 [1] 1129: 0.190 -0.0007707 -0.0006676 1994 6.64 -17.192 -18.621 2013-10-14T18:49:09.979633152 INFO 2025-06-26 20:01:38,051 calibrate.py _nudge_pos():1806 [1] 1373: 0.200 -0.0002545 -0.0002324 3104 10.34 -3.646 -4.163 2013-10-14T19:03:33.980444928 INFO 2025-06-26 20:01:38,098 calibrate.py _nudge_pos():1806 [1] 1378: 0.190 -0.0000209 0.0000026 99 0.33 -9.475 1.483 2013-10-14T19:03:57.978800896 INFO 2025-06-26 20:01:39,080 calibrate.py _nudge_pos():1806 [1] 1485: 0.190 -0.0000140 0.0000603 249 0.83 -2.511 13.510 2013-10-14T19:06:33.978114304 INFO 2025-06-26 20:01:39,108 calibrate.py _nudge_pos():1806 [1] 1488: 0.200 -0.0000485 -0.0000073 229 0.76 -9.455 -1.789 2013-10-14T19:07:21.974826240 INFO 2025-06-26 20:01:43,608 calibrate.py _nudge_pos():1806 [1] 1974: 0.010 0.0003663 -0.0003705 4625 15.41 3.521 -4.454 2013-10-14T19:30:52.178220800 INFO 2025-06-26 20:01:45,672 calibrate.py _nudge_pos():1806 [1] 2196: 0.200 0.0009294 -0.0000167 3724 12.41 11.097 -0.249 2013-10-14T19:46:57.982058496 INFO 2025-06-26 20:01:47,470 calibrate.py _nudge_pos():1806 [1] 2388: 0.010 -0.0005474 -0.0005462 1535 5.11 -15.864 -19.793 2013-10-14T19:55:16.177929984 INFO 2025-06-26 20:01:47,565 calibrate.py _nudge_pos():1806 [1] 2398: 0.200 0.0000048 0.0000111 69 0.23 3.152 9.072 2013-10-14T19:55:38.976367872 INFO 2025-06-26 20:01:48,673 calibrate.py _nudge_pos():1806 [1] 2517: 0.010 -0.0001285 -0.0001540 265 0.88 -21.633 -32.432 2013-10-14T19:58:30.174640128 INFO 2025-06-26 20:01:48,701 calibrate.py _nudge_pos():1806 [1] 2520: 0.010 0.0000081 0.0000568 130 0.43 2.787 24.466 2013-10-14T19:58:58.172722176 INFO 2025-06-26 20:01:49,572 calibrate.py _nudge_pos():1806 [1] 2613: 0.020 -0.0002013 -0.0001597 2060 6.86 -4.346 -4.311 2013-10-14T20:07:22.178195456 INFO 2025-06-26 20:01:52,411 calibrate.py _nudge_pos():1806 [1] 2917: 0.010 -0.0002247 -0.0003128 705 2.35 -14.185 -24.701 2013-10-14T20:14:46.177779456 INFO 2025-06-26 20:01:55,501 calibrate.py _nudge_pos():1806 [1] 3242: 0.010 0.0003096 -0.0001340 4140 13.80 3.325 -1.800 2013-10-14T20:33:58.178861824 INFO 2025-06-26 20:01:57,720 calibrate.py _nudge_pos():1806 [1] 3478: 0.030 0.0009714 -0.0000106 4075 13.58 10.600 -0.145 2013-10-14T20:51:28.176932096 INFO 2025-06-26 20:01:59,904 calibrate.py _nudge_pos():1806 [1] 3711: 0.020 -0.0004542 -0.0004651 1660 5.53 -12.170 -15.583 2013-10-14T21:00:52.178295296 INFO 2025-06-26 20:02:00,684 calibrate.py _nudge_pos():1806 [1] 3793: 0.020 -0.0000126 -0.0001724 265 0.88 -2.113 -36.290 2013-10-14T21:03:06.179115776 INFO 2025-06-26 20:02:00,751 calibrate.py _nudge_pos():1806 [1] 3800: 0.030 -0.0000096 0.0000251 125 0.41 -3.439 11.259 2013-10-14T21:03:37.176992256 INFO 2025-06-26 20:02:03,088 calibrate.py _nudge_pos():1862 [1] 4014: - - - 4 0.01 - - INFO 2025-06-26 20:02:03,088 calibrate.py _nudge_pos():1868 [1] Points in final series = 57650 INFO 2025-06-26 20:02:03,627 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:02:04,076 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:02:04,424 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:02:04,426 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.287.02/ctd1.nc INFO 2025-06-26 20:02:04,427 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:02:04,427 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 20:02:04,427 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:02:04,849 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:02:05,209 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:02:05,211 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.287.02/ctd2.nc INFO 2025-06-26 20:02:05,212 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:02:05,212 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 20:02:05,213 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:02:05,213 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.287.02 INFO 2025-06-26 20:02:05,223 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:02:05,779 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67] INFO 2025-06-26 20:02:05,881 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:02:16,361 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.287.02 ERROR 2025-06-26 20:02:16,361 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.287.02 INFO 2025-06-26 20:02:16,408 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_cal.nc INFO 2025-06-26 20:02:16,508 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:02:16,514 process.py align():251 [1] Alignment steps for 2013.287.02 INFO 2025-06-26 20:02:16,546 align.py process_cal():139 [1] Processing dorado_2013.287.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.287.02 INFO 2025-06-26 20:02:16,566 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:02:16,569 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:02:16,612 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:02:16,615 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:02:16,659 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:02:16,662 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:02:16,688 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:02:16,688 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:02:16,705 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:02:16,708 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:02:16,752 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:16,755 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:16,794 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:16,797 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:16,837 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:16,840 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:16,879 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:16,883 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:16,923 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:16,926 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:16,964 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:16,968 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,006 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,009 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,047 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,050 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,089 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,092 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,130 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,133 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,171 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,175 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,212 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,215 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,254 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,257 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,294 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,297 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,335 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,339 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,377 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,381 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,421 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,424 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,462 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,465 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,506 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,510 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,547 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,551 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,590 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,593 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,631 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:02:17,634 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:02:17,683 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:02:17,720 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:02:17,777 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:02:18,088 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:02:18,119 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_align.nc INFO 2025-06-26 20:02:18,219 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:02:18,222 process.py resample():273 [1] Resampling steps for 2013.287.02 INFO 2025-06-26 20:02:18,222 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:02:18,250 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_align.nc mission netCDF file INFO 2025-06-26 20:02:18,255 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_align.nc mission netCDF file INFO 2025-06-26 20:02:18,256 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-14T17:52:32.992342784 to 2013-10-14T21:07:45.979948032 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 20:02:18,258 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-14T17:52:05.404232448 to 2013-10-14T21:07:46.009945856 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:02:18,259 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-14T17:52:27.412724736 to 2013-10-14T21:07:45.899953664 (0 days 00:00:00.109992192 before mission_end) INFO 2025-06-26 20:02:18,261 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-14T17:52:27.952687872 to 2013-10-14T21:07:45.939950592 (0 days 00:00:00.069995264 before mission_end) INFO 2025-06-26 20:02:18,262 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-14T17:51:58.314683904 to 2013-10-14T21:07:44.620006912 (0 days 00:00:01.389938944 before mission_end) INFO 2025-06-26 20:02:18,263 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-14T17:52:02.254448384 to 2013-10-14T21:07:46.009945856 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:02:18,264 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_align.nc mission netCDF file INFO 2025-06-26 20:02:18,264 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,403 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,428 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,451 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,475 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,498 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,519 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,541 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,562 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,581 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,601 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,621 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,640 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,659 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,679 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,698 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,717 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,736 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,758 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,780 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,802 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,823 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,844 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,866 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,887 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,898 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,908 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:18,912 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:02:18,912 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:02:19,368 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:02:19,448 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:02:19,491 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:02:19,509 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:02:19,525 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:02:19,525 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:02:19,554 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:02:19,722 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_1S.nc INFO 2025-06-26 20:02:21,303 create_products.py gulper_odv():401 [1] No gulper times found for 2013.287.02 INFO 2025-06-26 20:02:21,303 process.py archive():337 [1] Archiving steps for 2013.287.02 INFO 2025-06-26 20:02:21,303 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02, BASE_PATH = /data/auv_data INFO 2025-06-26 20:02:21,304 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:02:21,305 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.02_1S.nc INFO 2025-06-26 20:02:21,322 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:02:21,323 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.02_cal.nc INFO 2025-06-26 20:02:21,406 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:02:21,407 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.02_align.nc INFO 2025-06-26 20:02:21,520 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:02:21,537 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,553 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,558 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,573 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,616 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,635 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,649 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,684 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,692 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.02 done. INFO 2025-06-26 20:02:21,692 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:02:21,692 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.02/dorado_2013.287.02_processing.log /Volumes/AUVCTD/surveys/2013/netcdf