INFO 2025-06-26 20:27:39,319 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 20:27:39,319 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB September 2014 with rhodamine sensor on ctdDriver2, channel 1 - ctdToUse = ctd1 INFO 2025-06-26 20:27:39,319 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.265.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:27:39,319 process.py download_process():165 [1] Download and processing steps for 2014.265.03 INFO 2025-06-26 20:27:39,320 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014265/2014.265.03 INFO 2025-06-26 20:27:39,320 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014265/2014.265.03 to /data/auv_data/dorado/missionlogs/2014.265.03 INFO 2025-06-26 20:27:45,146 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.265.03 INFO 2025-06-26 20:27:45,146 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/ctdDriver.log (11039526 bytes) INFO 2025-06-26 20:27:45,975 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/ctdDriver2.log (11046148 bytes) WARNING 2025-06-26 20:27:46,514 logs2netcdfs.py _read_data():216 [1] unpack requires a buffer of 8 bytes, b = b'\n' at record 115057, for time in file /data/auv_data/dorado/missionlogs/2014.265.03/ctdDriver2.log INFO 2025-06-26 20:27:46,515 logs2netcdfs.py _read_data():224 [1] bytes read = 11046155 file size = 11046148 INFO 2025-06-26 20:27:46,515 logs2netcdfs.py _read_data():229 [1] Tried to read 8 bytes, but only 7 bytes remaining INFO 2025-06-26 20:27:46,515 logs2netcdfs.py _read_data():235 [1] Successfully unpacked 115057 records WARNING 2025-06-26 20:27:46,528 logs2netcdfs.py _create_variable():536 [1] conductivity: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,529 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of conductivity.shape[0] (115058) WARNING 2025-06-26 20:27:46,529 logs2netcdfs.py _create_variable():544 [1] conductivity data is short by one, appending the last value: 4.396122425060191 WARNING 2025-06-26 20:27:46,540 logs2netcdfs.py _create_variable():536 [1] temperature: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,540 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of temperature.shape[0] (115058) WARNING 2025-06-26 20:27:46,540 logs2netcdfs.py _create_variable():544 [1] temperature data is short by one, appending the last value: 17.939824804251714 WARNING 2025-06-26 20:27:46,551 logs2netcdfs.py _create_variable():536 [1] cond_frequency: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,551 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of cond_frequency.shape[0] (115058) WARNING 2025-06-26 20:27:46,551 logs2netcdfs.py _create_variable():544 [1] cond_frequency data is short by one, appending the last value: 6358.5703125 WARNING 2025-06-26 20:27:46,562 logs2netcdfs.py _create_variable():536 [1] temp_frequency: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,562 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of temp_frequency.shape[0] (115058) WARNING 2025-06-26 20:27:46,563 logs2netcdfs.py _create_variable():544 [1] temp_frequency data is short by one, appending the last value: 8641.89453125 WARNING 2025-06-26 20:27:46,573 logs2netcdfs.py _create_variable():536 [1] rhodamine: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,573 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of rhodamine.shape[0] (115058) WARNING 2025-06-26 20:27:46,573 logs2netcdfs.py _create_variable():544 [1] rhodamine data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:27:46,584 logs2netcdfs.py _create_variable():536 [1] spare1: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,584 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of spare1.shape[0] (115058) WARNING 2025-06-26 20:27:46,584 logs2netcdfs.py _create_variable():544 [1] spare1 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:27:46,594 logs2netcdfs.py _create_variable():536 [1] spare2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,595 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of spare2.shape[0] (115058) WARNING 2025-06-26 20:27:46,595 logs2netcdfs.py _create_variable():544 [1] spare2 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:27:46,605 logs2netcdfs.py _create_variable():536 [1] flow2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,606 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of flow2.shape[0] (115058) WARNING 2025-06-26 20:27:46,606 logs2netcdfs.py _create_variable():544 [1] flow2 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:27:46,618 logs2netcdfs.py _create_variable():536 [1] spare3: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,618 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of spare3.shape[0] (115058) WARNING 2025-06-26 20:27:46,618 logs2netcdfs.py _create_variable():544 [1] spare3 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:27:46,629 logs2netcdfs.py _create_variable():536 [1] spare4: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,629 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of spare4.shape[0] (115058) WARNING 2025-06-26 20:27:46,629 logs2netcdfs.py _create_variable():544 [1] spare4 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:27:46,640 logs2netcdfs.py _create_variable():536 [1] salinity: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (115058,) and arg 1 with shape (115057,). INFO 2025-06-26 20:27:46,640 logs2netcdfs.py _create_variable():537 [1] len(data) (115057) does not match shape of salinity.shape[0] (115058) WARNING 2025-06-26 20:27:46,640 logs2netcdfs.py _create_variable():544 [1] salinity data is short by one, appending the last value: 33.39567883327457 INFO 2025-06-26 20:27:46,781 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.265.03/ctdDriver2.log: [115057] INFO 2025-06-26 20:27:46,812 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/gps.log (88340 bytes) INFO 2025-06-26 20:27:46,830 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/hydroscatlog.log (9665398 bytes) INFO 2025-06-26 20:27:47,818 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/navigation.log (41379138 bytes) INFO 2025-06-26 20:27:50,761 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/isuslog.log (716085 bytes) INFO 2025-06-26 20:27:50,830 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.265.03/isuslog.log: [1 2 3 4 6 7 8] INFO 2025-06-26 20:27:50,832 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/parosci.log (13553894 bytes) INFO 2025-06-26 20:27:51,953 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/tailCone.log (6908059 bytes) INFO 2025-06-26 20:27:52,789 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/biolume.log (8040746 bytes) INFO 2025-06-26 20:27:53,568 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:27:53,958 logs2netcdfs.py download_process_logs():807 [1] Time to process: 8.81 seconds INFO 2025-06-26 20:27:53,958 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.265.03/lopc.bin (36031392 bytes) INFO 2025-06-26 20:27:53,958 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:27:53 2025 INFO 2025-06-26 20:27:53,958 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.265.03/parosci.nc INFO 2025-06-26 20:27:53,958 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:27:53,958 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.265.03/parosci.nc INFO 2025-06-26 20:27:53,962 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1411397380.2, sensor_off_time = 1411426161.2 INFO 2025-06-26 20:27:53,962 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 28780 seconds. Expecting to read 57560 L frames from the lopc.bin file. INFO 2025-06-26 20:27:53,962 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 57560 records from the lopc.bin file. INFO 2025-06-26 20:27:54,305 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-09-22 14:49:40 Z and endTime = 2014-09-22 22:49:21 Z with 57560 records expected to be read from lopc.bin INFO 2025-06-26 20:27:54,306 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.265.03/lopc.bin INFO 2025-06-26 20:27:54,306 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.265.03/lopc.nc INFO 2025-06-26 20:27:54,306 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.265.03/lopc.nc INFO 2025-06-26 20:27:54,307 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.265.03 INFO 2025-06-26 20:27:54,307 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 20:27:54,340 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:27:54,340 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:27:54,340 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 20:28:00,187 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10146 15021 0 1 0 0 0 5.9 seconds, last L Frame: 57560 ERROR 2025-06-26 20:28:04,848 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x83 in position 0: invalid start byte INFO 2025-06-26 20:28:04,849 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 20:28:04,849 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.265.03/parosci.nc INFO 2025-06-26 20:28:04,849 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:28:04,849 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.265.03/parosci.nc INFO 2025-06-26 20:28:04,854 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1411397380.2, sensor_off_time = 1411426161.2 INFO 2025-06-26 20:28:04,854 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 28780 seconds. Expecting to read 57560 L frames from the lopc.bin file. INFO 2025-06-26 20:28:04,854 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 57560 records from the lopc.bin file. INFO 2025-06-26 20:28:04,855 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 60 and len(sampleCountList) = 16368 INFO 2025-06-26 20:28:04,857 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 20:28:04,857 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 60 61 62 ... 16512 16513 16514] INFO 2025-06-26 20:28:04,858 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 20:28:04,858 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 20:28:04,859 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 20:28:04,859 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 20:28:04,860 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 60 61 62 ... 16512 16513 16514] INFO 2025-06-26 20:28:04,860 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 60 61 62 ... 16512 16513 16514] with len(correctedSampleCountList) = 16368 INFO 2025-06-26 20:28:04,860 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 60 from all values of correctedSampleCountList INFO 2025-06-26 20:28:04,860 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 20:28:04,861 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.0000e+00 5.0000e-01 1.0000e+00 ... 8.2260e+03 8.2265e+03 8.2270e+03] INFO 2025-06-26 20:28:04,862 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.41139738e+09 1.41139738e+09 1.41139738e+09 ... 1.41140561e+09 1.41140561e+09 1.41140561e+09] INFO 2025-06-26 20:28:04,862 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1411397380.2 1411397380.7, ..., timestampArray[-2:] = 1411405606.7 1411405607.2] INFO 2025-06-26 20:28:04,880 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1411397380.1951377), np.float64(1411397380.6951377)], ..., timestampList[-2:] = [np.float64(1411405606.6951377), np.float64(1411405607.1951377)]] INFO 2025-06-26 20:28:04,880 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 16368) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:28:04,880 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [16337, 16358] INFO 2025-06-26 20:28:04,881 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 779 INFO 2025-06-26 20:28:04,881 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 16368 INFO 2025-06-26 20:28:04,881 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1411397380.1951377), np.float64(1411397380.6951377)], ..., timestampList[-2:] = [np.float64(1411405606.6951377), np.float64(1411405607.1951377)]] INFO 2025-06-26 20:28:04,881 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 16368) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:28:04,881 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(16336), np.int32(16357)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 20:28:04,882 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 779 INFO 2025-06-26 20:28:04,882 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 20:28:04,896 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 779 INFO 2025-06-26 20:28:04,896 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1411397433.1951377)], ..., tsList[-2:] = [np.float64(1411405591.6951377), np.float64(1411405602.1951377)] INFO 2025-06-26 20:28:04,897 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2014-09-22 14:50:33 Z INFO 2025-06-26 20:28:04,897 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2014-09-22 17:06:42 Z INFO 2025-06-26 20:28:04,897 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 779 INFO 2025-06-26 20:28:04,897 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.41139746e+09], ..., cFrameEsecsList[-2:] = [1.41140534e+09 1.41140534e+09] INFO 2025-06-26 20:28:04,897 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2014-09-22 14:50:57 Z INFO 2025-06-26 20:28:04,898 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2014-09-22 17:02:22 Z INFO 2025-06-26 20:28:04,902 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2014.265.03/lopc.nc INFO 2025-06-26 20:28:04,902 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 20:28:04 2025 Elapsed processing time from start of processing = 10 seconds INFO 2025-06-26 20:28:04,903 process.py calibrate():227 [1] Calibration steps for 2014.265.03 INFO 2025-06-26 20:28:05,136 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 20:28:05,139 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:28:06,416 calibrate.py _nudge_pos():1806 [1] 172: 0.140 -0.0005553 0.0011378 3110 10.36 -7.951 20.345 2014-09-22T15:02:51.700915712 INFO 2025-06-26 20:28:07,194 calibrate.py _nudge_pos():1806 [1] 255: 0.140 0.0003972 0.0037123 14420 48.06 1.226 14.312 2014-09-22T15:52:17.697731328 INFO 2025-06-26 20:28:08,058 calibrate.py _nudge_pos():1806 [1] 345: 0.150 -0.0004934 0.0053819 15085 50.28 -1.456 19.834 2014-09-22T16:44:03.694955776 INFO 2025-06-26 20:28:08,883 calibrate.py _nudge_pos():1806 [1] 431: 0.160 -0.0017967 0.0059281 14815 49.38 -5.401 22.245 2014-09-22T17:34:51.696153344 INFO 2025-06-26 20:28:09,881 calibrate.py _nudge_pos():1806 [1] 536: 0.170 -0.0021364 0.0049672 14895 49.65 -6.388 18.539 2014-09-22T18:26:15.694885120 INFO 2025-06-26 20:28:10,648 calibrate.py _nudge_pos():1806 [1] 614: 0.180 -0.0014878 0.0025504 9065 30.21 -7.311 15.642 2014-09-22T18:57:45.695411200 INFO 2025-06-26 20:28:11,488 calibrate.py _nudge_pos():1806 [1] 700: 0.190 -0.0062546 0.0020478 14935 49.78 -18.652 7.623 2014-09-22T19:48:57.694964736 INFO 2025-06-26 20:28:11,579 calibrate.py _nudge_pos():1806 [1] 709: 0.190 0.0000701 -0.0000233 115 0.38 27.387 -11.341 2014-09-22T19:49:28.692841216 INFO 2025-06-26 20:28:12,689 calibrate.py _nudge_pos():1806 [1] 822: 0.190 -0.0056408 0.0043210 14345 47.81 -17.511 16.746 2014-09-22T20:39:09.698628352 INFO 2025-06-26 20:28:12,760 calibrate.py _nudge_pos():1806 [1] 829: 0.190 0.0000955 0.0000009 180 0.60 23.765 0.290 2014-09-22T20:39:51.695751424 INFO 2025-06-26 20:28:14,127 calibrate.py _nudge_pos():1806 [1] 967: 0.200 -0.0045987 0.0041826 13895 46.31 -14.736 16.735 2014-09-22T21:28:27.695991808 INFO 2025-06-26 20:28:14,167 calibrate.py _nudge_pos():1806 [1] 971: 0.200 0.0001079 -0.0000209 151 0.50 32.016 -7.746 2014-09-22T21:29:01.693662720 INFO 2025-06-26 20:28:14,898 calibrate.py _nudge_pos():1806 [1] 1045: 0.010 -0.0047330 0.0026800 14675 48.91 -14.358 10.153 2014-09-22T22:19:09.897586688 INFO 2025-06-26 20:28:15,717 calibrate.py _nudge_pos():1806 [1] 1128: 0.200 -0.0000022 0.0000108 14 0.04 -7.660 46.023 2014-09-22T22:20:34.701777152 INFO 2025-06-26 20:28:15,757 calibrate.py _nudge_pos():1806 [1] 1132: 0.010 -0.0032019 0.0007187 8200 27.33 -17.384 4.873 2014-09-22T22:47:57.899210496 INFO 2025-06-26 20:28:16,572 calibrate.py _nudge_pos():1862 [1] 1167: - - - 1 0.00 - - INFO 2025-06-26 20:28:16,572 calibrate.py _nudge_pos():1868 [1] Points in final series = 143587 INFO 2025-06-26 20:28:17,891 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:28:18,956 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:28:19,795 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 34 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:28:19,798 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.265.03/ctd1.nc INFO 2025-06-26 20:28:19,799 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:28:19,800 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 20:28:19,800 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:28:20,817 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:28:21,664 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:28:21,666 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.265.03/ctd2.nc INFO 2025-06-26 20:28:21,668 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:28:21,668 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 20:28:21,668 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:28:22,732 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:28:24,272 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:28:24,325 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.265.03 INFO 2025-06-26 20:28:24,437 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_cal.nc INFO 2025-06-26 20:28:24,622 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, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, 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 20:28:24,629 process.py align():251 [1] Alignment steps for 2014.265.03 INFO 2025-06-26 20:28:24,677 align.py process_cal():139 [1] Processing dorado_2014.265.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.265.03 INFO 2025-06-26 20:28:24,718 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:28:24,724 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:28:24,828 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:28:24,835 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:28:24,934 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:28:24,943 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:28:24,999 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:28:24,999 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:28:25,037 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:28:25,044 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:28:25,140 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,145 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,229 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,234 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,317 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,323 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,404 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,410 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,492 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,498 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,578 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,583 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,664 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,669 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,749 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,755 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,836 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,842 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:25,920 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:25,926 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,009 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,014 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,094 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,100 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,180 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,186 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,265 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,270 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,352 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,357 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,437 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,443 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,524 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,530 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,611 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,617 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,698 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,704 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,786 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,792 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,874 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,879 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:26,960 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.265.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:28:26,965 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:28:27,067 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:28:27,136 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:28:27,204 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:28:27,274 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:28:27,347 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:28:27,470 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:28:28,189 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:28:28,250 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:28:28,310 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:28:28,370 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:28:28,430 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:28:28,494 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:28:28,563 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_align.nc INFO 2025-06-26 20:28:28,757 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, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, 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 20:28:28,760 process.py resample():273 [1] Resampling steps for 2014.265.03 INFO 2025-06-26 20:28:28,761 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:28:28,805 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_align.nc mission netCDF file INFO 2025-06-26 20:28:28,812 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_align.nc mission netCDF file INFO 2025-06-26 20:28:28,813 resample.py get_mission_start_end():1145 [1] navigation: 2014-09-22T14:50:26.911937536 to 2014-09-22T22:49:21.093511168 (0 days 00:00:00.159988992 before mission_end) INFO 2025-06-26 20:28:28,815 resample.py get_mission_start_end():1145 [1] hs2 : 2014-09-22T14:49:44.124868608 to 2014-09-22T22:49:21.253500160 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:28:28,817 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-09-22T14:50:14.652777216 to 2014-09-22T22:49:21.063513344 (0 days 00:00:00.189986816 before mission_end) INFO 2025-06-26 20:28:28,819 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-09-22T14:49:57.703938304 to 2014-09-22T22:49:21.083511808 (0 days 00:00:00.169988352 before mission_end) INFO 2025-06-26 20:28:28,821 resample.py get_mission_start_end():1145 [1] isus : 2014-09-22T14:50:40.171028992 to 2014-09-22T22:49:21.213502976 (0 days 00:00:00.039997184 before mission_end) INFO 2025-06-26 20:28:28,822 resample.py get_mission_start_end():1145 [1] biolume : 2014-09-22T14:49:37.915259648 to 2014-09-22T22:49:20.423522816 (0 days 00:00:00.829977344 before mission_end) INFO 2025-06-26 20:28:28,824 resample.py get_mission_start_end():1145 [1] lopc : 2014-09-22T14:50:33.195137792 to 2014-09-22T17:06:42.195137792 (0 days 05:42:39.058362368 before mission_end) WARNING 2025-06-26 20:28:28,825 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 05:42:39.058362368 INFO 2025-06-26 20:28:28,826 resample.py get_mission_start_end():1145 [1] tailcone : 2014-09-22T14:49:39.905157632 to 2014-09-22T22:49:21.253500160 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:28:28,827 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_align.nc mission netCDF file INFO 2025-06-26 20:28:28,828 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,127 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,179 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,229 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,279 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,323 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,367 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,410 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,451 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,491 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,529 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,568 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,607 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,646 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,687 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,726 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,766 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,805 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,847 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,889 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,930 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:29,972 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,015 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,057 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,099 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,119 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,136 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,151 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,167 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,182 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:30,188 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:28:30,188 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:28:31,211 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:28:31,474 resample.py add_biolume_proxies():633 [1] Zero flow values found: 28784 of 28784 - replaced with 350 ml/s INFO 2025-06-26 20:28:31,475 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:28:31,576 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:28:31,621 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:28:31,657 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:28:31,657 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:28:31,675 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:31,675 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 05:42:39.058362368 of NaNs to the end of mission INFO 2025-06-26 20:28:31,686 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:31,686 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 05:42:39.058362368 of NaNs to the end of mission INFO 2025-06-26 20:28:31,696 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:31,697 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 05:42:39.058362368 of NaNs to the end of mission INFO 2025-06-26 20:28:31,706 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:31,707 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 05:42:39.058362368 of NaNs to the end of mission INFO 2025-06-26 20:28:31,717 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:31,717 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 05:42:39.058362368 of NaNs to the end of mission INFO 2025-06-26 20:28:31,763 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:28:32,053 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_1S.nc INFO 2025-06-26 20:28:36,246 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:29:06,190 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.265.03/dorado_2014.265.03_1S_Gulper.txt INFO 2025-06-26 20:29:06,190 process.py archive():337 [1] Archiving steps for 2014.265.03 INFO 2025-06-26 20:29:06,190 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03, BASE_PATH = /data/auv_data INFO 2025-06-26 20:29:06,192 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:29:06,193 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.265.03_1S.nc INFO 2025-06-26 20:29:06,224 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:29:06,225 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.265.03_cal.nc INFO 2025-06-26 20:29:06,403 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:29:06,404 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.265.03_align.nc INFO 2025-06-26 20:29:06,659 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:29:06,693 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,724 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,729 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,756 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,864 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,872 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,909 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:06,935 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:07,021 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:07,050 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014265/2014.265.03 done. INFO 2025-06-26 20:29:07,050 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:29:07,052 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.265.03_1S_Gulper.txt INFO 2025-06-26 20:29:07,056 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.265.03/dorado_2014.265.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:29:07,057 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.265.03/dorado_2014.265.03_processing.log /Volumes/AUVCTD/surveys/2014/netcdf