INFO 2025-06-26 19:58:27,010 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 19:58:27,010 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Autonomy group's short missions in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 19:58:27,010 process.py process_mission():449 [1] Processing AUVCTD mission 2013.283.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:58:27,010 process.py download_process():165 [1] Download and processing steps for 2013.283.00 INFO 2025-06-26 19:58:27,010 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013283/2013.283.00 INFO 2025-06-26 19:58:27,010 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013283/2013.283.00 to /data/auv_data/dorado/missionlogs/2013.283.00 INFO 2025-06-26 19:58:30,282 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.283.00 INFO 2025-06-26 19:58:30,283 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/ctdDriver.log (5979366 bytes) INFO 2025-06-26 19:58:30,710 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/ctdDriver2.log (5985599 bytes) INFO 2025-06-26 19:58:31,140 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/gps.log (349268 bytes) INFO 2025-06-26 19:58:31,185 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/hydroscatlog.log (5242294 bytes) INFO 2025-06-26 19:58:31,721 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/navigation.log (21185398 bytes) INFO 2025-06-26 19:58:33,218 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/parosci.log (7370870 bytes) INFO 2025-06-26 19:58:33,832 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/tailCone.log (3747403 bytes) INFO 2025-06-26 19:58:34,290 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/biolume.log (4362662 bytes) INFO 2025-06-26 19:58:34,718 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:58:34,938 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.65 seconds INFO 2025-06-26 19:58:34,938 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.283.00/lopc.bin (25173663 bytes) INFO 2025-06-26 19:58:34,938 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:58:34 2025 INFO 2025-06-26 19:58:34,938 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.283.00/parosci.nc INFO 2025-06-26 19:58:34,938 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:58:34,938 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.283.00/parosci.nc INFO 2025-06-26 19:58:34,942 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381418126.4, sensor_off_time = 1381433738.1 INFO 2025-06-26 19:58:34,942 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 15611 seconds. Expecting to read 31222 L frames from the lopc.bin file. INFO 2025-06-26 19:58:34,942 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 31222 records from the lopc.bin file. INFO 2025-06-26 19:58:35,123 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-10 15:15:26 Z and endTime = 2013-10-10 19:35:38 Z with 31222 records expected to be read from lopc.bin INFO 2025-06-26 19:58:35,123 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.283.00/lopc.bin INFO 2025-06-26 19:58:35,123 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.283.00/lopc.nc INFO 2025-06-26 19:58:35,123 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.283.00/lopc.nc INFO 2025-06-26 19:58:35,124 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.283.00 INFO 2025-06-26 19:58:35,124 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:58:35,177 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:58:35,177 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:58:35,177 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:58:41,323 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 19:58:41,324 process.py calibrate():227 [1] Calibration steps for 2013.283.00 INFO 2025-06-26 19:58:41,565 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 19:58:41,567 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:58:42,278 calibrate.py _nudge_pos():1806 [1] 106: 0.150 -0.0003852 -0.0007189 3419 11.40 -5.009 -11.688 2013-10-10T15:28:33.909841664 INFO 2025-06-26 19:58:44,342 calibrate.py _nudge_pos():1806 [1] 328: 0.160 0.0008146 0.0002665 5735 19.11 6.315 2.584 2013-10-10T15:51:21.906127616 INFO 2025-06-26 19:58:46,418 calibrate.py _nudge_pos():1806 [1] 551: 0.150 0.0007571 0.0001367 3150 10.50 10.689 2.414 2013-10-10T16:05:33.907761664 INFO 2025-06-26 19:58:48,484 calibrate.py _nudge_pos():1806 [1] 772: 0.160 -0.0008099 -0.0007690 3310 11.03 -10.880 -12.919 2013-10-10T16:20:15.907340544 INFO 2025-06-26 19:58:49,469 calibrate.py _nudge_pos():1806 [1] 878: 0.160 0.0001852 -0.0003869 1775 5.91 4.640 -12.123 2013-10-10T16:27:57.905691392 INFO 2025-06-26 19:58:49,498 calibrate.py _nudge_pos():1806 [1] 881: 0.160 -0.0000082 -0.0000079 70 0.23 -5.278 -6.333 2013-10-10T16:28:13.904595456 INFO 2025-06-26 19:58:58,077 calibrate.py _nudge_pos():1806 [1] 1801: 0.160 0.0000037 -0.0000010 15 0.05 11.696 -3.936 2013-10-10T16:43:35.901434368 INFO 2025-06-26 19:58:58,139 calibrate.py _nudge_pos():1806 [1] 1807: 0.160 -0.0008089 -0.0004920 5785 19.28 -6.216 -4.729 2013-10-10T17:02:57.901831936 INFO 2025-06-26 19:58:59,981 calibrate.py _nudge_pos():1806 [1] 2004: 0.160 0.0015863 0.0000238 5350 17.83 13.184 0.247 2013-10-10T17:24:03.905104640 INFO 2025-06-26 19:59:02,072 calibrate.py _nudge_pos():1806 [1] 2227: 0.160 -0.0009828 -0.0008239 3060 10.20 -14.282 -14.972 2013-10-10T17:37:57.907971584 INFO 2025-06-26 19:59:02,083 calibrate.py _nudge_pos():1806 [1] 2228: 0.160 -0.0000157 -0.0000251 115 0.38 -6.123 -12.217 2013-10-10T17:38:20.906396160 INFO 2025-06-26 19:59:02,955 calibrate.py _nudge_pos():1806 [1] 2321: 0.170 0.0001350 -0.0004449 1915 6.38 3.136 -12.921 2013-10-10T17:46:15.903856640 INFO 2025-06-26 19:59:10,828 calibrate.py _nudge_pos():1806 [1] 3157: 0.180 0.0000155 -0.0001639 7620 25.40 0.090 -1.196 2013-10-10T18:25:34.902254080 INFO 2025-06-26 19:59:12,911 calibrate.py _nudge_pos():1806 [1] 3378: 0.180 -0.0002595 0.0001167 3330 11.10 -3.466 1.948 2013-10-10T18:40:21.901490432 INFO 2025-06-26 19:59:14,651 calibrate.py _nudge_pos():1806 [1] 3562: 0.170 0.0013086 0.0000174 5775 19.25 10.077 0.168 2013-10-10T19:02:39.909830656 INFO 2025-06-26 19:59:16,752 calibrate.py _nudge_pos():1806 [1] 3783: 0.180 -0.0015335 -0.0009558 3100 10.33 -22.002 -17.145 2013-10-10T19:16:39.902287360 INFO 2025-06-26 19:59:18,030 calibrate.py _nudge_pos():1806 [1] 3918: 0.170 0.0000477 -0.0001496 290 0.96 7.332 -28.777 2013-10-10T19:19:51.909133824 INFO 2025-06-26 19:59:18,069 calibrate.py _nudge_pos():1806 [1] 3922: 0.180 -0.0000062 0.0000300 135 0.45 -2.068 12.437 2013-10-10T19:20:21.907078656 INFO 2025-06-26 19:59:26,759 calibrate.py _nudge_pos():1862 [1] 4802: - - - 1 0.00 - - INFO 2025-06-26 19:59:26,759 calibrate.py _nudge_pos():1868 [1] Points in final series = 77879 INFO 2025-06-26 19:59:26,987 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 3 of 62396 INFO 2025-06-26 19:59:27,457 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:59:28,049 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:59:28,508 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 42 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:59:28,510 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.283.00/ctd1.nc INFO 2025-06-26 19:59:28,511 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:59:28,511 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 19:59:28,511 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:59:29,073 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:59:29,533 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 19:59:29,535 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.283.00/ctd2.nc WARNING 2025-06-26 19:59:29,537 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1397) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 19:59:29,537 calibrate.py _range_qc_combined_nc():898 [1] Setting 1397 ctd2_salinity values to NaN INFO 2025-06-26 19:59:29,537 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 19:59:29,537 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 19:59:29,538 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.283.00 INFO 2025-06-26 19:59:29,550 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:59:30,275 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62] INFO 2025-06-26 19:59:30,410 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:59:44,465 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.283.00 ERROR 2025-06-26 19:59:44,466 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.283.00 INFO 2025-06-26 19:59:44,529 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_cal.nc INFO 2025-06-26 19:59:44,648 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 19:59:44,654 process.py align():251 [1] Alignment steps for 2013.283.00 INFO 2025-06-26 19:59:44,689 align.py process_cal():139 [1] Processing dorado_2013.283.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.283.00 INFO 2025-06-26 19:59:44,714 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:59:44,718 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:59:44,773 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:59:44,778 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:59:44,832 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:59:44,837 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:59:44,872 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:59:44,873 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:59:44,895 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:59:44,900 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:59:44,955 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:44,959 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,007 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,012 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,062 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,066 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,114 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,118 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,167 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,171 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,218 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,222 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,271 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,275 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,321 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,325 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,373 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,377 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,424 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,428 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,476 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,480 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,529 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,533 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,581 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,585 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,633 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,636 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,685 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,689 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,736 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,740 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,789 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,793 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,841 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,845 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,894 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,899 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:45,947 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:45,951 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:46,000 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:46,005 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:46,054 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.283.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:59:46,058 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:59:46,122 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:59:46,169 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:59:46,245 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:59:46,648 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:59:46,688 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_align.nc INFO 2025-06-26 19:59:46,807 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 19:59:46,810 process.py resample():273 [1] Resampling steps for 2013.283.00 INFO 2025-06-26 19:59:46,810 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:59:46,842 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_align.nc mission netCDF file INFO 2025-06-26 19:59:46,847 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_align.nc mission netCDF file INFO 2025-06-26 19:59:46,848 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-10T15:16:02.311329792 to 2013-10-10T19:35:38.114314240 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 19:59:46,850 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-10T15:15:32.023404800 to 2013-10-10T19:35:38.004321792 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 19:59:46,852 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-10T15:16:09.120863488 to 2013-10-10T19:35:38.024320256 (0 days 00:00:00.129991424 before mission_end) INFO 2025-06-26 19:59:46,853 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-10T15:15:52.751984896 to 2013-10-10T19:35:38.144312064 (0 days 00:00:00.009999616 before mission_end) INFO 2025-06-26 19:59:46,855 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-10T15:15:25.233835776 to 2013-10-10T19:35:36.944360192 (0 days 00:00:01.209951488 before mission_end) INFO 2025-06-26 19:59:46,857 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-10T15:15:26.373791744 to 2013-10-10T19:35:38.154311680 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:59:46,858 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_align.nc mission netCDF file INFO 2025-06-26 19:59:46,858 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,034 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,065 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,098 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,130 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,158 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,184 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,209 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,235 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,259 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,283 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,307 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,330 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,353 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,377 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,400 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,424 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,449 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,475 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,501 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,531 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,556 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,581 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,606 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,632 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,646 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,657 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:47,661 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:59:47,662 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:59:48,255 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:59:48,357 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:59:48,413 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:59:48,437 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:59:48,458 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:59:48,458 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:59:48,492 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:59:48,683 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_1S.nc INFO 2025-06-26 19:59:49,809 create_products.py gulper_odv():401 [1] No gulper times found for 2013.283.00 INFO 2025-06-26 19:59:49,809 process.py archive():337 [1] Archiving steps for 2013.283.00 INFO 2025-06-26 19:59:49,810 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00, BASE_PATH = /data/auv_data INFO 2025-06-26 19:59:49,812 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:59:49,816 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.283.00_1S.nc INFO 2025-06-26 19:59:49,837 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:59:49,838 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.283.00_cal.nc INFO 2025-06-26 19:59:49,952 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:59:49,954 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.283.00_align.nc INFO 2025-06-26 19:59:50,100 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:59:50,123 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,143 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,149 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,168 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,224 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,249 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,265 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,310 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,324 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013283/2013.283.00 done. INFO 2025-06-26 19:59:50,325 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:59:50,325 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.283.00/dorado_2013.283.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf