INFO 2025-06-26 18:57:15,180 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 18:57:15,180 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX mission - Maria Fox's algorithm in Monterey Bay - ctdToUse = ctd1 INFO 2025-06-26 18:57:15,180 process.py process_mission():449 [1] Processing CANON September 2011 mission 2011.285.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 18:57:15,180 process.py download_process():165 [1] Download and processing steps for 2011.285.01 INFO 2025-06-26 18:57:15,180 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011285/2011.285.01 INFO 2025-06-26 18:57:15,180 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011285/2011.285.01 to /data/auv_data/dorado/missionlogs/2011.285.01 INFO 2025-06-26 18:57:20,079 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.285.01 INFO 2025-06-26 18:57:20,079 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/ctdDriver.log (9779814 bytes) INFO 2025-06-26 18:57:20,859 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/ctdDriver2.log (9779519 bytes) INFO 2025-06-26 18:57:21,696 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/gps.log (252572 bytes) INFO 2025-06-26 18:57:21,734 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/hydroscatlog.log (8560882 bytes) INFO 2025-06-26 18:57:22,749 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/navigation.log (34621654 bytes) INFO 2025-06-26 18:57:25,584 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/isuslog.log (809493 bytes) INFO 2025-06-26 18:57:25,674 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/parosci.log (10338518 bytes) INFO 2025-06-26 18:57:26,650 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/tailCone.log (6117835 bytes) INFO 2025-06-26 18:57:27,464 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/biolume.log (7121722 bytes) INFO 2025-06-26 18:57:28,189 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:57:28,584 logs2netcdfs.py download_process_logs():807 [1] Time to process: 8.51 seconds INFO 2025-06-26 18:57:28,585 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.285.01/lopc.bin (110091000 bytes) INFO 2025-06-26 18:57:28,585 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:57:28 2025 INFO 2025-06-26 18:57:28,585 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.285.01/parosci.nc INFO 2025-06-26 18:57:28,585 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:57:28,585 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.285.01/parosci.nc INFO 2025-06-26 18:57:28,590 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1318431576.0, sensor_off_time = 1318457069.2 INFO 2025-06-26 18:57:28,590 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 25493 seconds. Expecting to read 50986 L frames from the lopc.bin file. INFO 2025-06-26 18:57:28,590 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 50986 records from the lopc.bin file. INFO 2025-06-26 18:57:28,901 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-10-12 14:59:36 Z and endTime = 2011-10-12 22:04:29 Z with 50986 records expected to be read from lopc.bin INFO 2025-06-26 18:57:28,901 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.285.01/lopc.bin INFO 2025-06-26 18:57:28,901 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.285.01/lopc.nc INFO 2025-06-26 18:57:28,901 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.285.01/lopc.nc INFO 2025-06-26 18:57:28,902 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.285.01 INFO 2025-06-26 18:57:28,902 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 18:57:28,906 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0224131 WARNING 2025-06-26 18:57:28,906 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 18:57:29,008 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 18:57:29,008 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 18:57:29,008 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 18:57:29,371 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 18:57:29,372 process.py calibrate():227 [1] Calibration steps for 2011.285.01 INFO 2025-06-26 18:57:29,606 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 18:57:29,608 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:57:30,280 calibrate.py _nudge_pos():1806 [1] 98: 0.140 -0.0005614 -0.0015479 4340 14.46 -5.756 -19.831 2011-10-12T15:15:40.969255168 INFO 2025-06-26 18:57:32,019 calibrate.py _nudge_pos():1806 [1] 275: 0.150 -0.0014559 -0.0017811 3830 12.76 -16.915 -25.858 2011-10-12T15:31:22.964723968 INFO 2025-06-26 18:57:32,910 calibrate.py _nudge_pos():1806 [1] 364: 0.140 -0.0030966 -0.0029737 8200 27.33 -16.800 -20.162 2011-10-12T16:00:10.966348032 INFO 2025-06-26 18:57:33,597 calibrate.py _nudge_pos():1806 [1] 433: 0.150 -0.0000532 -0.0000904 440 1.46 -5.386 -11.448 2011-10-12T16:02:46.965660928 INFO 2025-06-26 18:57:39,088 calibrate.py _nudge_pos():1806 [1] 971: 0.140 0.0005151 -0.0009287 1995 6.65 11.489 -25.890 2011-10-12T16:18:22.971540480 INFO 2025-06-26 18:57:39,780 calibrate.py _nudge_pos():1806 [1] 1038: 0.150 0.0036074 -0.0001216 5790 19.30 27.723 -1.168 2011-10-12T16:38:46.967691008 INFO 2025-06-26 18:57:41,815 calibrate.py _nudge_pos():1806 [1] 1193: 0.160 0.0004046 -0.0019563 4570 15.23 3.939 -23.802 2011-10-12T16:56:34.964528128 INFO 2025-06-26 18:57:42,865 calibrate.py _nudge_pos():1806 [1] 1288: 0.150 0.0003225 -0.0019025 4570 15.23 3.140 -23.147 2011-10-12T17:13:22.965475328 INFO 2025-06-26 18:57:43,917 calibrate.py _nudge_pos():1806 [1] 1370: 0.150 -0.0001940 -0.0017686 4665 15.55 -1.851 -21.080 2011-10-12T17:30:16.966011648 INFO 2025-06-26 18:57:45,584 calibrate.py _nudge_pos():1806 [1] 1518: 0.160 -0.0003554 -0.0018717 5505 18.35 -2.873 -18.904 2011-10-12T17:51:04.970517504 INFO 2025-06-26 18:57:46,643 calibrate.py _nudge_pos():1806 [1] 1607: 0.160 0.0001439 -0.0015185 4690 15.63 1.365 -18.002 2011-10-12T18:08:10.970231552 INFO 2025-06-26 18:57:47,610 calibrate.py _nudge_pos():1806 [1] 1699: 0.160 -0.0000388 -0.0005954 1165 3.88 -1.483 -28.434 2011-10-12T18:13:34.968036096 INFO 2025-06-26 18:57:48,194 calibrate.py _nudge_pos():1806 [1] 1752: 0.160 0.0000474 -0.0009715 3190 10.63 0.661 -16.934 2011-10-12T18:25:04.970767616 INFO 2025-06-26 18:57:49,217 calibrate.py _nudge_pos():1806 [1] 1833: 0.160 0.0003988 -0.0021470 4580 15.26 3.874 -26.065 2011-10-12T18:41:40.972537088 INFO 2025-06-26 18:57:49,914 calibrate.py _nudge_pos():1806 [1] 1894: 0.170 -0.0001082 -0.0000065 90 0.30 -54.071 -4.066 2011-10-12T18:42:58.967193856 INFO 2025-06-26 18:57:50,200 calibrate.py _nudge_pos():1806 [1] 1913: 0.170 0.0001859 -0.0012757 4680 15.60 1.768 -15.157 2011-10-12T18:58:52.971840256 INFO 2025-06-26 18:57:51,745 calibrate.py _nudge_pos():1806 [1] 2054: 0.170 0.0005600 -0.0013986 4760 15.86 5.235 -16.337 2011-10-12T19:17:04.967033344 INFO 2025-06-26 18:57:53,675 calibrate.py _nudge_pos():1806 [1] 2234: 0.160 0.0002508 -0.0016423 4595 15.31 2.429 -19.873 2011-10-12T19:35:22.971814912 INFO 2025-06-26 18:57:55,305 calibrate.py _nudge_pos():1806 [1] 2388: 0.170 0.0002507 -0.0009038 4605 15.35 2.422 -10.912 2011-10-12T19:53:16.968240896 INFO 2025-06-26 18:57:56,852 calibrate.py _nudge_pos():1806 [1] 2545: 0.180 0.0002326 -0.0009648 4680 15.60 2.212 -11.463 2011-10-12T20:11:28.963434240 INFO 2025-06-26 18:57:58,392 calibrate.py _nudge_pos():1806 [1] 2702: 0.180 0.0010669 -0.0013825 4855 16.18 9.779 -15.833 2011-10-12T20:30:16.966160896 INFO 2025-06-26 18:57:59,811 calibrate.py _nudge_pos():1806 [1] 2847: 0.190 -0.0006298 -0.0024714 6360 21.20 -4.406 -21.605 2011-10-12T20:53:52.969157888 INFO 2025-06-26 18:57:59,912 calibrate.py _nudge_pos():1806 [1] 2857: 0.180 -0.0000118 0.0000662 75 0.25 -7.116 49.715 2011-10-12T20:54:16.967514112 INFO 2025-06-26 18:58:00,096 calibrate.py _nudge_pos():1806 [1] 2875: 0.190 -0.0000155 0.0000215 65 0.21 -10.764 18.712 2011-10-12T20:54:46.965458944 INFO 2025-06-26 18:58:01,316 calibrate.py _nudge_pos():1806 [1] 3000: 0.190 0.0020089 -0.0014406 4480 14.93 19.955 -17.880 2011-10-12T21:11:46.965584384 INFO 2025-06-26 18:58:02,178 calibrate.py _nudge_pos():1806 [1] 3087: 0.190 0.0006747 -0.0015940 4665 15.55 6.437 -18.998 2011-10-12T21:28:46.965709568 INFO 2025-06-26 18:58:04,766 calibrate.py _nudge_pos():1806 [1] 3348: 0.190 -0.0001060 -0.0026925 8505 28.35 -0.555 -17.600 2011-10-12T22:01:27.971371264 INFO 2025-06-26 18:58:05,726 calibrate.py _nudge_pos():1806 [1] 3445: 0.200 0.0000125 -0.0000161 64 0.21 8.813 -14.230 2011-10-12T22:03:16.963904768 INFO 2025-06-26 18:58:06,229 calibrate.py _nudge_pos():1862 [1] 3458: - - - 111 0.37 - - INFO 2025-06-26 18:58:06,229 calibrate.py _nudge_pos():1868 [1] Points in final series = 127147 INFO 2025-06-26 18:58:06,471 calibrate.py _depth_process():2162 [1] Removing depths outside of valid_depth_range=Range(min=-1, max=25) for self.args.mission=2011.285.01 INFO 2025-06-26 18:58:06,475 calibrate.py _depth_process():2175 [1] Setting 2 depths values to NaN WARNING 2025-06-26 18:58:06,478 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:58:06,650 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 32 of 101903 INFO 2025-06-26 18:58:07,425 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:58:08,366 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:58:09,141 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:58:09,143 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.285.01/ctd1.nc INFO 2025-06-26 18:58:09,145 calibrate.py _range_qc_combined_nc():898 [1] Setting 304 ctd1_salinity values to NaN INFO 2025-06-26 18:58:09,145 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 18:58:09,145 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 18:58:10,036 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:58:10,782 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:58:10,784 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.285.01/ctd2.nc WARNING 2025-06-26 18:58:10,786 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1988) ctd2_salinity values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 18:58:10,786 calibrate.py _range_qc_combined_nc():898 [1] Setting 1988 ctd2_salinity values to NaN INFO 2025-06-26 18:58:10,786 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 18:58:10,786 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 18:58:10,831 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 18:58:12,199 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 18:58:12,239 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.285.01 ERROR 2025-06-26 18:58:12,240 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.285.01 INFO 2025-06-26 18:58:12,339 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_cal.nc INFO 2025-06-26 18:58:12,505 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 18:58:12,511 process.py align():251 [1] Alignment steps for 2011.285.01 INFO 2025-06-26 18:58:12,553 align.py process_cal():139 [1] Processing dorado_2011.285.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.285.01 INFO 2025-06-26 18:58:12,590 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:58:12,594 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:58:12,677 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:58:12,683 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:58:12,768 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:58:12,774 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:58:12,823 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 18:58:12,823 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 18:58:12,855 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:58:12,860 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:58:12,941 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:12,946 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,018 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,023 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,096 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,101 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,172 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,177 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,250 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,255 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,326 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,331 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,405 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,410 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,482 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,487 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,561 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,566 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,637 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,642 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,717 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,722 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,793 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,798 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,871 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,876 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:13,949 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:13,953 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,027 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,032 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,104 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,109 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,183 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,188 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,268 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,273 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,346 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,352 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,424 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,430 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,504 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,509 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,580 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.285.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:58:14,585 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:58:14,673 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:58:14,734 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:58:14,795 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.99 INFO 2025-06-26 18:58:14,860 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:58:14,924 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:58:15,031 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 18:58:15,667 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:58:15,725 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_align.nc INFO 2025-06-26 18:58:15,896 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 18:58:15,899 process.py resample():273 [1] Resampling steps for 2011.285.01 INFO 2025-06-26 18:58:15,899 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 18:58:15,939 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_align.nc mission netCDF file INFO 2025-06-26 18:58:15,945 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_align.nc mission netCDF file INFO 2025-06-26 18:58:15,946 resample.py get_mission_start_end():1145 [1] navigation: 2011-10-12T15:00:13.982758144 to 2011-10-12T22:04:29.198956288 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 18:58:15,948 resample.py get_mission_start_end():1145 [1] hs2 : 2011-10-12T14:59:41.464985600 to 2011-10-12T22:04:29.228954368 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 18:58:15,950 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-10-12T15:00:03.533474048 to 2011-10-12T22:04:29.228954368 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 18:58:15,952 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-10-12T15:00:03.473478144 to 2011-10-12T22:04:29.148960000 (0 days 00:00:00.099992832 before mission_end) INFO 2025-06-26 18:58:15,953 resample.py get_mission_start_end():1145 [1] isus : 2011-10-12T15:00:53.670039296 to 2011-10-12T22:04:29.248952832 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:58:15,955 resample.py get_mission_start_end():1145 [1] biolume : 2011-10-12T14:59:35.265376000 to 2011-10-12T22:04:28.138994688 (0 days 00:00:01.109958144 before mission_end) INFO 2025-06-26 18:58:15,956 resample.py get_mission_start_end():1145 [1] tailcone : 2011-10-12T14:59:40.165074944 to 2011-10-12T22:04:29.138960384 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 18:58:15,957 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_align.nc mission netCDF file INFO 2025-06-26 18:58:15,957 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,232 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,280 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,325 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,372 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,413 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,454 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,492 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,529 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,565 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,603 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,638 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,673 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,708 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,743 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,778 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,814 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,851 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,889 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,928 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:16,973 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,011 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,049 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,087 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,125 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,145 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,162 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,178 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,192 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,206 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:17,211 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 18:58:17,211 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 18:58:18,150 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 18:58:18,320 resample.py add_biolume_proxies():633 [1] Zero flow values found: 1 of 25494 - replaced with 350 ml/s INFO 2025-06-26 18:58:18,320 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 18:58:18,412 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 18:58:18,453 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 18:58:18,491 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 18:58:18,491 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 18:58:18,541 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 18:58:18,800 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_1S.nc INFO 2025-06-26 18:58:20,130 create_products.py gulper_odv():401 [1] No gulper times found for 2011.285.01 INFO 2025-06-26 18:58:20,130 process.py archive():337 [1] Archiving steps for 2011.285.01 INFO 2025-06-26 18:58:20,130 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01, BASE_PATH = /data/auv_data INFO 2025-06-26 18:58:20,132 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 18:58:20,133 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.285.01_1S.nc INFO 2025-06-26 18:58:20,158 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:58:20,159 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.285.01_cal.nc INFO 2025-06-26 18:58:20,324 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:58:20,325 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.285.01_align.nc INFO 2025-06-26 18:58:20,551 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:58:20,582 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,611 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,618 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,644 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,744 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,752 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,781 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,804 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,876 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,882 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011285/2011.285.01 done. INFO 2025-06-26 18:58:20,882 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 18:58:20,882 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.285.01/dorado_2011.285.01_processing.log /Volumes/AUVCTD/surveys/2011/netcdf