INFO 2025-06-26 16:26:32,897 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 16:26:32,897 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey fifth - M0 to LatMix, aborted at 2000 local - serial interface hardware failure first rhodamin.log file - ctdToUse = ctd1 INFO 2025-06-26 16:26:32,897 process.py process_mission():449 [1] Processing AUVCTD mission 2010.284.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:26:32,897 process.py download_process():165 [1] Download and processing steps for 2010.284.00 INFO 2025-06-26 16:26:32,897 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010284/2010.284.00 INFO 2025-06-26 16:26:32,898 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010284/2010.284.00 to /data/auv_data/dorado/missionlogs/2010.284.00 INFO 2025-06-26 16:26:45,546 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.284.00 INFO 2025-06-26 16:26:45,548 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/ctdDriver.log (21883691 bytes) INFO 2025-06-26 16:26:47,076 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.284.00/ctdDriver.log: [ 476 498 599 671 1421 1510 1646 1965 2222 2271 2312 3014 3361 3404 3992 4591 4818 5117 6226 6943 7751 7884 9273 10419 11367 11828 11889 12901 16701 22906 25644 25656 26985 28660 29627 31257 31734 34413 36350 39609 41396 41913 43621 46921 52948 56276 61269 63895 64409 65301 65798 67817 69801 75308 79411 81272] INFO 2025-06-26 16:26:47,143 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/ctdDriver2.log (21891263 bytes) INFO 2025-06-26 16:26:48,736 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.284.00/ctdDriver2.log: [ 227 568 740 1025 1131 1491 1584 1716 1732 2035 2341 2694 3084 3431 3474 4062 4661 5187 6201 7317 8685 9343 10489 11044 11898 11972 12972 12990 16772 17128 22977 27055 28730 31327 34483 38625 41466 43691 45902 47104 54539 54653 56983 58026 61339 64479 65869 72958 74889 75266 75479 78568 79481 81874 85354] INFO 2025-06-26 16:26:48,813 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/gps.log (70772 bytes) INFO 2025-06-26 16:26:48,829 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/hydroscatlog.log (19165126 bytes) INFO 2025-06-26 16:26:50,773 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.284.00/hydroscatlog.log: [ 66 360 572 592 649 787 849 940 1040 1205 1409 1511 1661 1797 2235 2296 2321 2373 3607 4969 7363 8714 8764 10032 10952 11121 11587 11975 12049 13067 19521 21583 25786 29312 31639 32425 32907 35738 38691 39745 41531 43203 48031 49437 49919 51075 56636 58083 64534 71750 72909 73991 75424 75428 75529 76785 77009 79483 87023 87103 87347 87529 89229 89870 90691 91497 92854 94463 94603 99991 100251 101637 102125 102403 104029 104529 105357 105617 106147 108448 108933 110513 110691 110756 111289 111404 111760 111938 111998 112015 112887 113064 113363 113541 113595 113719 113772 114305 114482 114610 114789 114838 114967 116081 116211 116585 117613 117708 118741 120326 120556 120862 120912 121268 121396 121978 123761 124258 124295 124437 124473 124974 125186 125332 125612 126031 126098 126566 126814 127101 128426 128699 128784 129142 129234 129321 129946 130124 130576 130934 131611 131872 131911 132151 132331 133232 133344 133521 133588 133878 134416 134595 134774 135668 136642 136741 136821 137001 137538 137634 137994 138414 138441 138572 138984 139217 139796 140154 140512 140691 141326 141504 141584 141684 142302 142481 142840 143198 143378 144387 144567 144815 144928 144958 145291 145354 145829 146073 146191 146371 146792 147458 148053 148951 149081 149982 150031 150391 151068 151429 151609 153243 153996 154327 154537 154689 154704 154872 155053 155415 155959 156321 156343 156523 156703 156883 157226 157405 157422 157783 157871 158131 158675 159933 160297 160744 160839 161021 161202 161437 161925 162106 162471 162563 162651 162925 163013 164922 165104 165465 165647 165723 166456 166557 166741 166813 166995 167105 167652 168081 168196 168378 169349 169651 169933 170019 170201 170383 170441 170623 170749 170805 170931 171113 171167 171477 171659 172023 172255 172617 172982 173163 173272 173345 173707 173891 174255 174577 174759 175123 175305 175853 176035 176217 176796 177522 178072 178254 178411 178593 178618 178958 178981 179323 179344 180053 180072 180256 180801 181333 181699 181711 182075 182249 182615 182988 183164 183529 184082 184582 184626 185173 185181 185355 185362 185545 186266 186642 187194 187547 187562 187912 188462 188482 188828 189216 190103 190129 190468 191016 191046 191595 191778 191928 192111 192145 192329 192513 192697 192845 193431 193614 193701 193759 194166 194488 194716 194854 195451 196349 197052 197087 197602 198008 198335 198518 198559 198886 198929 199069 199112 200402 200908 202007 202192 202744 202875 203543 203911 204217 204466 204584 204652 205021 205501 206672 206856 207101 207225 207595 207728 207782 208027 208154 208211 209863 210001 210418 211481 211666 211851 211893 212038 212224 212449 212633 212783 213003 213737 214261 214293 214478 214632 214817 215373 215558 215647 215745 215771 216301 216671 216693 217061 217411 217596 218337 218521 218905 219263 219275 219449 220009 220202 220387 220752 220937 221496 221681 222385 222426 222986 224093 224281 224341 224485 224671 224841 224857 225581 225599 225954 226161 226347 226511 226721 227465 227776 227841 227998] INFO 2025-06-26 16:26:50,840 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/navigation.log (66708830 bytes) INFO 2025-06-26 16:26:55,652 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/isuslog.log (1420437 bytes) INFO 2025-06-26 16:26:55,788 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.284.00/isuslog.log: [1] INFO 2025-06-26 16:26:55,792 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/parosci.log (9519926 bytes) INFO 2025-06-26 16:26:56,611 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/tailCone.log (13654843 bytes) INFO 2025-06-26 16:26:58,329 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/biolume.log (15915498 bytes) INFO 2025-06-26 16:26:59,914 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:27:00,709 logs2netcdfs.py download_process_logs():807 [1] Time to process: 15.16 seconds INFO 2025-06-26 16:27:00,709 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.284.00/lopc.bin (113554404 bytes) INFO 2025-06-26 16:27:00,710 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:27:00 2025 INFO 2025-06-26 16:27:00,710 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.284.00/parosci.nc INFO 2025-06-26 16:27:00,710 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:27:00,710 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.284.00/parosci.nc INFO 2025-06-26 16:27:00,713 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1286832337.5, sensor_off_time = 1286854077.7 INFO 2025-06-26 16:27:00,713 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 21740 seconds. Expecting to read 43480 L frames from the lopc.bin file. INFO 2025-06-26 16:27:00,714 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 43480 records from the lopc.bin file. INFO 2025-06-26 16:27:00,968 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-11 21:25:37 Z and endTime = 2010-10-12 03:27:57 Z with 43480 records expected to be read from lopc.bin INFO 2025-06-26 16:27:00,968 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.284.00/lopc.bin INFO 2025-06-26 16:27:00,968 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.284.00/lopc.nc INFO 2025-06-26 16:27:00,968 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.284.00/lopc.nc INFO 2025-06-26 16:27:00,969 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.284.00 INFO 2025-06-26 16:27:00,969 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 16:27:01,125 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:27:01,125 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:27:01,125 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:27:01,561 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 16:27:01,563 process.py calibrate():227 [1] Calibration steps for 2010.284.00 INFO 2025-06-26 16:27:01,959 calibrate.py _navigation_process():1649 [1] Removing points outside of time range for 2010.284.00/navigation.nc WARNING 2025-06-26 16:27:01,964 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (174371) navigation_time values found outside of range. This may indicate a problem with the navigation data. INFO 2025-06-26 16:27:01,965 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('navigation_time', Range(min=Timestamp('2010-10-11 20:00:00'), max=Timestamp('2010-10-12 03:28:00')))] INFO 2025-06-26 16:27:01,966 calibrate.py _range_qc_combined_nc():916 [1] navigation_time: deleting 174371 values found outside of above ranges: ['2010-10-12T03:28:00.108804864' '2010-10-12T03:28:00.318790656' '2010-10-12T03:28:00.518776832' ... '2010-10-12T13:17:33.715546880' '2010-10-12T13:17:33.915533312' '2010-10-12T13:17:34.115519488'] INFO 2025-06-26 16:27:01,977 calibrate.py _range_qc_combined_nc():916 [1] navigation_roll: deleting 174371 values found outside of above ranges: [-3.3350812 -3.3350812 -3.3350812 ... -3.3350812 -3.3350812 -3.3350812] INFO 2025-06-26 16:27:01,982 calibrate.py _range_qc_combined_nc():916 [1] navigation_pitch: deleting 174371 values found outside of above ranges: [20.24230956 20.24230956 20.24230956 ... 20.24230956 20.24230956 20.24230956] INFO 2025-06-26 16:27:01,988 calibrate.py _range_qc_combined_nc():916 [1] navigation_yaw: deleting 174371 values found outside of above ranges: [167.44304192 167.44304192 167.44304192 ... 167.44304192 167.44304192 167.44304192] INFO 2025-06-26 16:27:01,994 calibrate.py _range_qc_combined_nc():916 [1] navigation_posx: deleting 174371 values found outside of above ranges: [ 4390.88344174 4390.62060247 4390.3577635 ... -42100.11789579 -42100.38073507 -42100.64357403] INFO 2025-06-26 16:27:01,999 calibrate.py _range_qc_combined_nc():916 [1] navigation_posy: deleting 174371 values found outside of above ranges: [-1002.1360281 -1002.07748385 -1002.01893966 ... 9353.17001696 9353.22856122 9353.28710541] INFO 2025-06-26 16:27:02,005 calibrate.py _range_qc_combined_nc():916 [1] navigation_depth: deleting 174371 values found outside of above ranges: [40.59406903 40.59406903 40.59406903 ... 40.59406903 40.59406903 40.59406903] INFO 2025-06-26 16:27:02,011 calibrate.py _range_qc_combined_nc():916 [1] navigation_mWaterSpeed: deleting 174371 values found outside of above ranges: [1.43512981 1.43512981 1.43512981 ... 1.43512981 1.43512981 1.43512981] INFO 2025-06-26 16:27:02,017 calibrate.py _range_qc_combined_nc():916 [1] navigation_latitude: deleting 174371 values found outside of above ranges: [36.87222004 36.87221766 36.87221529 ... 36.45207743 36.45207505 36.45207268] INFO 2025-06-26 16:27:02,023 calibrate.py _range_qc_combined_nc():916 [1] navigation_longitude: deleting 174371 values found outside of above ranges: [-121.91100005 -121.91099943 -121.91099881 ... -121.80135072 -121.8013501 -121.80134949] INFO 2025-06-26 16:27:02,034 calibrate.py _range_qc_combined_nc():936 [1] Done range checking navigation INFO 2025-06-26 16:27:02,037 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 16:27:02,039 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:27:02,926 calibrate.py _nudge_pos():1806 [1] 131: 0.170 0.0001572 -0.0003393 994 3.36 6.932 -18.691 2010-10-11T21:31:04.105901824 INFO 2025-06-26 16:27:03,541 calibrate.py _nudge_pos():1806 [1] 194: 0.170 -0.0032883 -0.0006537 9423 31.56 -15.446 -3.838 2010-10-11T22:03:40.111906048 INFO 2025-06-26 16:27:04,262 calibrate.py _nudge_pos():1806 [1] 270: 0.180 -0.0026020 0.0002857 12203 40.75 -9.464 1.299 2010-10-11T22:45:40.109274368 INFO 2025-06-26 16:27:04,934 calibrate.py _nudge_pos():1806 [1] 341: 0.190 -0.0023420 -0.0003414 9417 31.43 -11.040 -2.013 2010-10-11T23:18:16.105279744 INFO 2025-06-26 16:27:05,721 calibrate.py _nudge_pos():1806 [1] 423: 0.190 0.0009768 0.0001467 9629 32.15 4.503 0.846 2010-10-11T23:51:46.107585024 INFO 2025-06-26 16:27:06,259 calibrate.py _nudge_pos():1806 [1] 479: 0.180 0.0000334 0.0000315 15 0.05 106.188 125.220 2010-10-11T23:52:44.113611264 INFO 2025-06-26 16:27:06,434 calibrate.py _nudge_pos():1806 [1] 497: 0.190 0.0010023 0.0001929 9635 32.15 4.623 1.112 2010-10-12T00:25:10.110301440 INFO 2025-06-26 16:27:07,119 calibrate.py _nudge_pos():1806 [1] 569: 0.190 0.0017557 0.0000768 9890 33.01 7.887 0.431 2010-10-12T00:59:22.109729792 INFO 2025-06-26 16:27:07,795 calibrate.py _nudge_pos():1806 [1] 639: 0.200 -0.0035880 -0.0009052 9325 31.11 -17.098 -5.391 2010-10-12T01:31:40.106967808 INFO 2025-06-26 16:27:08,492 calibrate.py _nudge_pos():1806 [1] 710: 0.200 -0.0020594 -0.0006735 11281 37.63 -8.112 -3.317 2010-10-12T02:10:28.107488768 INFO 2025-06-26 16:27:09,189 calibrate.py _nudge_pos():1806 [1] 781: 0.190 -0.0029236 -0.0004589 9323 31.13 -13.916 -2.732 2010-10-12T02:42:46.114726400 INFO 2025-06-26 16:27:10,255 calibrate.py _nudge_pos():1806 [1] 889: 0.010 0.0011447 0.0002453 9504 31.71 5.350 1.433 2010-10-12T03:16:16.307018752 INFO 2025-06-26 16:27:11,062 calibrate.py _nudge_pos():1862 [1] 921: - - - 3112 10.37 - - INFO 2025-06-26 16:27:11,062 calibrate.py _nudge_pos():1868 [1] Points in final series = 108040 WARNING 2025-06-26 16:27:11,216 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:27:40,045 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1399 of 227695 INFO 2025-06-26 16:27:41,733 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 9 seconds, d_end_time_diff: 35332 seconds INFO 2025-06-26 16:27:57,834 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 46 seconds, d_end_time_diff: 35317 seconds INFO 2025-06-26 16:27:59,539 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 46 seconds, d_end_time_diff: 35317 seconds INFO 2025-06-26 16:27:59,542 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.284.00/ctd1.nc WARNING 2025-06-26 16:27:59,544 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (1834) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 16:27:59,544 calibrate.py _range_qc_combined_nc():898 [1] Setting 1834 ctd1_salinity values to NaN INFO 2025-06-26 16:27:59,544 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 16:27:59,544 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:27:59,544 calibrate.py _ctd_process():2929 [1] Removing points outside of time range for 2010.284.00/ctd1.nc WARNING 2025-06-26 16:27:59,549 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (141166) ctd1_time values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 16:27:59,549 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_time', Range(min=Timestamp('2010-10-11 20:00:00'), max=Timestamp('2010-10-12 03:28:00')))] INFO 2025-06-26 16:27:59,550 calibrate.py _range_qc_combined_nc():916 [1] ctd1_time: deleting 141166 values found outside of above ranges: ['2010-10-12T03:28:00.038809856' '2010-10-12T03:28:00.288792576' '2010-10-12T03:28:00.538775552' ... '2010-10-12T13:16:34.529601536' '2010-10-12T13:16:34.779584512' '2010-10-12T13:16:35.029567232'] INFO 2025-06-26 16:27:59,561 calibrate.py _range_qc_combined_nc():916 [1] ctd1_temperature: deleting 141166 values found outside of above ranges: [11.23185714 11.26622149 11.3085999 ... 14.05482752 14.05474081 14.055131 ] INFO 2025-06-26 16:27:59,566 calibrate.py _range_qc_combined_nc():916 [1] ctd1_conductivity: deleting 141166 values found outside of above ranges: [3.80209214 3.80379922 3.80728947 ... 0.05000851 0.05014254 0.0503158 ] INFO 2025-06-26 16:27:59,571 calibrate.py _range_qc_combined_nc():916 [1] ctd1_salinity: deleting 141166 values found outside of above ranges: [33.75082817 33.73622978 33.731922 ... nan nan nan] INFO 2025-06-26 16:27:59,575 calibrate.py _range_qc_combined_nc():916 [1] ctd1_temperature_onboard: deleting 141166 values found outside of above ranges: [11.23185714 11.26622149 11.3085999 ... 14.05482752 14.05474081 14.055131 ] INFO 2025-06-26 16:27:59,584 calibrate.py _range_qc_combined_nc():916 [1] ctd1_conductivity_onboard: deleting 141166 values found outside of above ranges: [3.80210459 3.80381168 3.80730195 ... 0.05000868 0.0501427 0.05031597] INFO 2025-06-26 16:27:59,592 calibrate.py _range_qc_combined_nc():916 [1] ctd1_salinity_onboard: deleting 141166 values found outside of above ranges: [33.75386217 33.7392599 33.73494844 ... 0.30929492 0.31015044 0.31125273] INFO 2025-06-26 16:27:59,601 calibrate.py _range_qc_combined_nc():916 [1] ctd1_dissolvedO2: deleting 141166 values found outside of above ranges: [2.41147741 2.41147741 2.41147741 ... 3.5030525 3.5030525 3.5030525 ] INFO 2025-06-26 16:27:59,607 calibrate.py _range_qc_combined_nc():916 [1] ctd1_oxygen_mll: deleting 141166 values found outside of above ranges: [3.60010997 3.5978755 3.59481416 ... 6.78178412 6.78176082 6.78165863] INFO 2025-06-26 16:27:59,612 calibrate.py _range_qc_combined_nc():916 [1] ctd1_oxygen_umolkg: deleting 141166 values found outside of above ranges: [156.54818318 156.45370462 156.32227062 ... 302.65208421 302.65083938 302.64603683] INFO 2025-06-26 16:27:59,621 calibrate.py _range_qc_combined_nc():916 [1] ctd1_flow1: deleting 141166 values found outside of above ranges: [0. 0. 0. ... 0. 0. 0.] INFO 2025-06-26 16:27:59,627 calibrate.py _range_qc_combined_nc():916 [1] ctd1_depth: deleting 141166 values found outside of above ranges: [39.03878024 39.03878024 39.03878024 ... 39.03878024 39.03878024 39.03878024] INFO 2025-06-26 16:27:59,644 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:28:12,158 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: 35317 seconds INFO 2025-06-26 16:28:13,859 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: 35317 seconds INFO 2025-06-26 16:28:13,863 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.284.00/ctd2.nc INFO 2025-06-26 16:28:13,865 calibrate.py _range_qc_combined_nc():898 [1] Setting 303 ctd2_salinity values to NaN INFO 2025-06-26 16:28:13,865 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 16:28:13,865 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:28:13,865 calibrate.py _ctd_process():2929 [1] Removing points outside of time range for 2010.284.00/ctd2.nc WARNING 2025-06-26 16:28:13,870 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (141174) ctd2_time values found outside of range. This may indicate a problem with the ctd2 data. INFO 2025-06-26 16:28:13,870 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_time', Range(min=Timestamp('2010-10-11 20:00:00'), max=Timestamp('2010-10-12 03:28:00')))] INFO 2025-06-26 16:28:13,871 calibrate.py _range_qc_combined_nc():916 [1] ctd2_time: deleting 141174 values found outside of above ranges: ['2010-10-12T03:28:00.208798208' '2010-10-12T03:28:00.458780928' '2010-10-12T03:28:00.708763904' ... '2010-10-12T13:16:34.649593344' '2010-10-12T13:16:34.899576064' '2010-10-12T13:16:35.149559040'] INFO 2025-06-26 16:28:13,883 calibrate.py _range_qc_combined_nc():916 [1] ctd2_temperature: deleting 141174 values found outside of above ranges: [11.22129413 11.27980092 11.32544108 ... 14.01122114 14.01085336 14.01122114] INFO 2025-06-26 16:28:13,889 calibrate.py _range_qc_combined_nc():916 [1] ctd2_conductivity: deleting 141174 values found outside of above ranges: [3.79788806 3.80279948 3.8060334 ... 4.024689 4.02478937 4.0247571 ] INFO 2025-06-26 16:28:13,896 calibrate.py _range_qc_combined_nc():916 [1] ctd2_salinity: deleting 141174 values found outside of above ranges: [33.71892052 33.71392619 33.70412835 ... 33.4016793 33.40292812 33.40230999] INFO 2025-06-26 16:28:13,903 calibrate.py _range_qc_combined_nc():916 [1] ctd2_temperature_onboard: deleting 141174 values found outside of above ranges: [11.22129413 11.27980092 11.32544108 ... 14.01122114 14.01085336 14.01122114] INFO 2025-06-26 16:28:13,914 calibrate.py _range_qc_combined_nc():916 [1] ctd2_conductivity_onboard: deleting 141174 values found outside of above ranges: [3.7979005 3.80281193 3.80604587 ... 4.02470218 4.02480255 4.02477029] INFO 2025-06-26 16:28:13,925 calibrate.py _range_qc_combined_nc():916 [1] ctd2_salinity_onboard: deleting 141174 values found outside of above ranges: [33.72195283 33.71695349 33.70715127 ... 33.40447851 33.40572744 33.40510924] INFO 2025-06-26 16:28:13,935 calibrate.py _range_qc_combined_nc():916 [1] ctd2_flow2: deleting 141174 values found outside of above ranges: [0. 0. 0. ... 0. 0. 0.] INFO 2025-06-26 16:28:13,943 calibrate.py _range_qc_combined_nc():916 [1] ctd2_depth: deleting 141174 values found outside of above ranges: [39.03878024 39.03878024 39.03878024 ... 39.03878024 39.03878024 39.03878024] INFO 2025-06-26 16:28:13,960 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:28:16,102 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:28:18,761 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3361684 3361685 3361686] INFO 2025-06-26 16:28:19,240 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: 35242 seconds INFO 2025-06-26 16:29:11,615 calibrate.py _biolume_process():3193 [1] Removing points outside of time range for 2010.284.00/biolume.nc WARNING 2025-06-26 16:29:11,618 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (34648) biolume_time values found outside of range. This may indicate a problem with the biolume data. INFO 2025-06-26 16:29:11,618 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('biolume_time', Range(min=Timestamp('2010-10-11 20:00:00'), max=Timestamp('2010-10-12 03:28:00')))] INFO 2025-06-26 16:29:11,618 calibrate.py _range_qc_combined_nc():936 [1] Done range checking biolume WARNING 2025-06-26 16:29:11,673 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (2071332) biolume_time60hz values found outside of range. This may indicate a problem with the biolume data. INFO 2025-06-26 16:29:11,674 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('biolume_time60hz', Range(min=Timestamp('2010-10-11 20:00:00'), max=Timestamp('2010-10-12 03:28:00')))] INFO 2025-06-26 16:29:11,674 calibrate.py _range_qc_combined_nc():936 [1] Done range checking biolume ERROR 2025-06-26 16:29:11,674 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2010.284.00 ERROR 2025-06-26 16:29:11,674 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.284.00 INFO 2025-06-26 16:29:11,892 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_cal.nc INFO 2025-06-26 16:29:21,637 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 16:29:21,645 process.py align():251 [1] Alignment steps for 2010.284.00 INFO 2025-06-26 16:29:21,728 align.py process_cal():139 [1] Processing dorado_2010.284.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.284.00 INFO 2025-06-26 16:29:21,760 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:29:21,764 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:29:21,839 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:29:21,844 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:29:21,921 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:29:21,927 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:29:21,971 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:29:21,971 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:29:21,999 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:29:22,004 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:29:22,086 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,094 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:29:22,217 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,226 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:29:22,350 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,359 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 3.99 INFO 2025-06-26 16:29:22,473 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,479 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,544 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,549 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,612 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,617 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,682 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,686 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,750 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,755 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,819 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,824 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,893 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,898 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:22,962 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:22,967 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,032 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,037 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,101 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,106 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,169 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,173 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,238 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,243 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,308 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,313 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,379 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,384 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,448 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,453 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,519 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,523 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,589 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,594 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,660 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,665 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,728 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.284.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:29:23,733 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:29:23,814 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:29:23,878 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:29:23,944 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:29:24,014 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:29:24,088 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:29:24,283 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.84 INFO 2025-06-26 16:29:25,652 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.98 INFO 2025-06-26 16:29:25,770 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_align.nc INFO 2025-06-26 16:29:26,062 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 16:29:26,068 process.py resample():273 [1] Resampling steps for 2010.284.00 INFO 2025-06-26 16:29:26,069 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:29:26,146 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_align.nc mission netCDF file INFO 2025-06-26 16:29:26,154 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_align.nc mission netCDF file INFO 2025-06-26 16:29:26,155 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-11T21:26:22.755175680 to 2010-10-12T03:27:59.918818048 (0 days 09:49:34.286695424 before mission_end) WARNING 2025-06-26 16:29:26,156 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 09:49:34.286695424 INFO 2025-06-26 16:29:26,158 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-11T21:25:46.667647744 to 2010-10-12T13:11:16.781368832 (0 days 00:06:17.424144640 before mission_end) WARNING 2025-06-26 16:29:26,160 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 00:06:17.424144640 INFO 2025-06-26 16:29:26,161 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-11T21:26:23.995090688 to 2010-10-12T03:27:59.798826240 (0 days 09:49:34.406687232 before mission_end) WARNING 2025-06-26 16:29:26,162 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 09:49:34.406687232 INFO 2025-06-26 16:29:26,163 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-11T21:26:06.686276352 to 2010-10-12T03:27:59.958815232 (0 days 09:49:34.246698240 before mission_end) WARNING 2025-06-26 16:29:26,164 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 09:49:34.246698240 INFO 2025-06-26 16:29:26,165 resample.py get_mission_start_end():1145 [1] isus : 2010-10-11T21:26:35.424307712 to 2010-10-12T13:16:49.088604160 (0 days 00:00:45.116909312 before mission_end) INFO 2025-06-26 16:29:26,167 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-11T21:25:33.888488960 to 2010-10-12T13:15:19.644697088 (0 days 00:02:14.560816384 before mission_end) INFO 2025-06-26 16:29:26,169 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-11T21:25:37.528273920 to 2010-10-12T13:17:34.205513472 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:29:26,170 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_align.nc mission netCDF file INFO 2025-06-26 16:29:26,171 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,411 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,411 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 09:49:34.286695424 of NaNs to the end of mission INFO 2025-06-26 16:29:26,454 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,455 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 09:49:34.286695424 of NaNs to the end of mission INFO 2025-06-26 16:29:26,497 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,498 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 09:49:34.286695424 of NaNs to the end of mission INFO 2025-06-26 16:29:26,540 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,541 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 09:49:34.286695424 of NaNs to the end of mission INFO 2025-06-26 16:29:26,615 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,615 resample.py resample_variable():1038 [1] Padding hs2_bbp420 with 0 days 00:06:17.424144640 of NaNs to the end of mission INFO 2025-06-26 16:29:26,696 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,696 resample.py resample_variable():1038 [1] Padding hs2_bbp700 with 0 days 00:06:17.424144640 of NaNs to the end of mission INFO 2025-06-26 16:29:26,776 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,776 resample.py resample_variable():1038 [1] Padding hs2_fl700 with 0 days 00:06:17.424144640 of NaNs to the end of mission INFO 2025-06-26 16:29:26,821 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,821 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:26,857 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,857 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:26,894 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,894 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:26,930 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,930 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:26,966 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:26,966 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:27,003 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,003 resample.py resample_variable():1038 [1] Padding ctd1_salinity_onboard with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:27,041 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,041 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:27,077 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,077 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:27,112 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,113 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:27,148 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,148 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 09:49:34.406687232 of NaNs to the end of mission INFO 2025-06-26 16:29:27,186 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,186 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,224 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,224 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,261 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,262 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,298 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,299 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,336 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,336 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,372 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,372 resample.py resample_variable():1038 [1] Padding ctd2_salinity_onboard with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,409 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,409 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 09:49:34.246698240 of NaNs to the end of mission INFO 2025-06-26 16:29:27,436 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,461 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,485 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,509 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,533 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:27,540 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:29:27,541 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:29:29,743 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:29:30,515 resample.py add_biolume_proxies():633 [1] Zero flow values found: 507 of 56987 - replaced with 350 ml/s INFO 2025-06-26 16:29:30,515 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:29:30,794 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:29:30,888 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:29:30,919 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:29:30,919 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:29:31,020 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:29:31,267 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_1S.nc INFO 2025-06-26 16:31:15,843 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 16:31:18,365 create_products.py gulper_odv():522 [1] Wrote 2 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.284.00/dorado_2010.284.00_1S_Gulper.txt INFO 2025-06-26 16:31:18,365 process.py archive():337 [1] Archiving steps for 2010.284.00 INFO 2025-06-26 16:31:18,365 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00, BASE_PATH = /data/auv_data INFO 2025-06-26 16:31:18,366 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:31:18,367 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.284.00_1S.nc INFO 2025-06-26 16:31:18,391 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:31:18,392 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.284.00_cal.nc INFO 2025-06-26 16:31:18,627 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:31:18,629 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.284.00_align.nc INFO 2025-06-26 16:31:19,041 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:31:19,113 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,175 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,185 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,237 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,409 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,419 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,447 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,498 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,670 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,676 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010284/2010.284.00 done. INFO 2025-06-26 16:31:19,676 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:31:19,678 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.284.00_1S_Gulper.txt INFO 2025-06-26 16:31:19,683 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.284.00/dorado_2010.284.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 16:31:19,683 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.284.00/dorado_2010.284.00_processing.log /Volumes/AUVCTD/surveys/2010/netcdf