INFO 2025-06-26 06:08:54,850 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2003 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 06:08:54,850 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Re-portaled 8/22/05 - ctdToUse = ctd1 INFO 2025-06-26 06:08:54,851 process.py process_mission():449 [1] Processing BIOLUME mission 2004.321.00 by user docker_user on host 671049448ece INFO 2025-06-26 06:08:54,851 process.py download_process():165 [1] Download and processing steps for 2004.321.00 INFO 2025-06-26 06:08:54,851 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2004/2004321/2004.321.00 INFO 2025-06-26 06:08:54,851 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2004/2004321/2004.321.00 to /data/auv_data/dorado/missionlogs/2004.321.00 INFO 2025-06-26 06:08:57,058 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2004.321.00 INFO 2025-06-26 06:08:57,058 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/ctdDriver.log (6387083 bytes) INFO 2025-06-26 06:08:57,518 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/ctdDriver2.log (6386989 bytes) INFO 2025-06-26 06:08:57,981 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/gps.log (60548 bytes) INFO 2025-06-26 06:08:57,996 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/hydroscatlog.log (4356674 bytes) INFO 2025-06-26 06:08:58,512 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/navigation.log (14150143 bytes) INFO 2025-06-26 06:08:59,613 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/isuslog.log (374741 bytes) INFO 2025-06-26 06:08:59,653 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.321.00/isuslog.log: [1 2 3 4 6 7] INFO 2025-06-26 06:08:59,654 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/parosci.log (4359014 bytes) INFO 2025-06-26 06:09:00,025 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/tailCone.log (4358875 bytes) INFO 2025-06-26 06:09:00,577 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2004.321.00/biolume.log (4365196 bytes) INFO 2025-06-26 06:09:00,998 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 06:09:01,273 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2004.321.00/biolume.log: [3] INFO 2025-06-26 06:09:01,288 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.23 seconds WARNING 2025-06-26 06:09:01,288 process.py download_process():196 [1] No lopc.bin file for 2004.321.00 INFO 2025-06-26 06:09:01,288 process.py calibrate():227 [1] Calibration steps for 2004.321.00 INFO 2025-06-26 06:09:01,452 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 06:09:01,454 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 06:09:03,006 calibrate.py _nudge_pos():1806 [1] 181: 0.070 0.0034583 0.0026880 11347 37.83 13.576 13.166 2004-11-16T18:16:31.798473856 INFO 2025-06-26 06:09:03,667 calibrate.py _nudge_pos():1806 [1] 252: 0.080 0.0032740 0.0016167 11320 37.73 12.886 7.940 2004-11-16T18:55:25.798583808 INFO 2025-06-26 06:09:04,360 calibrate.py _nudge_pos():1806 [1] 326: 0.070 0.0020586 -0.0000554 13135 43.78 6.982 -0.235 2004-11-16T19:40:25.803620864 INFO 2025-06-26 06:09:04,810 calibrate.py _nudge_pos():1806 [1] 373: 0.070 0.0012893 0.0008146 11290 37.63 5.087 4.011 2004-11-16T20:18:49.795786624 INFO 2025-06-26 06:09:06,051 calibrate.py _nudge_pos():1806 [1] 503: 0.070 0.0018797 0.0017647 11325 37.75 7.393 8.663 2004-11-16T20:58:43.801785984 INFO 2025-06-26 06:09:06,693 calibrate.py _nudge_pos():1806 [1] 570: 0.080 0.0034975 0.0016753 11340 37.80 13.736 8.213 2004-11-16T21:37:37.801895808 INFO 2025-06-26 06:09:07,352 calibrate.py _nudge_pos():1806 [1] 638: 0.080 0.0046069 0.0003417 11128 37.10 18.433 1.707 2004-11-16T22:15:50.804814336 INFO 2025-06-26 06:09:07,373 calibrate.py _nudge_pos():1806 [1] 640: 0.070 0.0045753 0.0003185 375 1.25 544.783 47.340 2004-11-16T22:17:06.799608448 INFO 2025-06-26 06:09:07,985 calibrate.py _nudge_pos():1806 [1] 704: 0.090 0.0023863 0.0000565 5450 18.16 19.501 0.576 2004-11-16T22:36:19.800622464 INFO 2025-06-26 06:09:09,191 calibrate.py _nudge_pos():1862 [1] 808: - - - 2 0.00 - - INFO 2025-06-26 06:09:09,191 calibrate.py _nudge_pos():1868 [1] Points in final series = 90698 WARNING 2025-06-26 06:09:09,264 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 5.00 Hz INFO 2025-06-26 06:09:09,985 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:09:10,645 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:09:11,199 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:09:11,202 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2004.321.00/ctd1.nc INFO 2025-06-26 06:09:11,203 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 06:09:11,204 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 06:09:11,204 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 06:09:11,828 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:09:12,360 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 06:09:12,363 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2004.321.00/ctd2.nc INFO 2025-06-26 06:09:12,364 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 06:09:12,364 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 06:09:12,365 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 06:09:12,929 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 06:09:13,613 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863] INFO 2025-06-26 06:09:13,753 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: 0 seconds ERROR 2025-06-26 06:09:14,007 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 06:09:14,008 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.321.00 ERROR 2025-06-26 06:09:14,008 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2004.321.00 INFO 2025-06-26 06:09:14,081 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_cal.nc INFO 2025-06-26 06:09:14,163 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 06:09:14,168 process.py align():251 [1] Alignment steps for 2004.321.00 INFO 2025-06-26 06:09:14,195 align.py process_cal():139 [1] Processing dorado_2004.321.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2004.321.00 INFO 2025-06-26 06:09:14,222 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:09:14,225 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:09:14,292 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:09:14,296 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:09:14,360 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:09:14,365 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:09:14,403 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 06:09:14,403 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 06:09:14,429 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 06:09:14,433 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:09:14,495 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:09:14,499 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,556 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:09:14,560 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,615 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 06:09:14,619 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,676 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:14,680 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,797 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:14,801 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,858 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:14,862 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,919 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:14,923 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:14,981 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:14,985 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,043 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,047 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,104 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,108 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,164 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,168 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,224 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,228 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,285 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,289 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,346 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,350 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,408 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,412 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,469 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,473 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,531 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,535 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,592 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,596 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,654 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,658 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,716 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2004.321.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 06:09:15,720 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 06:09:15,783 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:09:15,823 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:09:15,864 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.65 INFO 2025-06-26 06:09:15,907 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.88 INFO 2025-06-26 06:09:15,952 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 06:09:15,996 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_align.nc INFO 2025-06-26 06:09:16,070 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, 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 06:09:16,072 process.py resample():273 [1] Resampling steps for 2004.321.00 INFO 2025-06-26 06:09:16,073 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 06:09:16,098 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_align.nc mission netCDF file INFO 2025-06-26 06:09:16,103 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_align.nc mission netCDF file INFO 2025-06-26 06:09:16,104 resample.py get_mission_start_end():1145 [1] navigation: 2004-11-16T17:36:03.604816384 to 2004-11-16T22:38:24.202100224 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 06:09:16,106 resample.py get_mission_start_end():1145 [1] hs2 : 2004-11-16T17:35:46.935958400 to 2004-11-16T22:38:24.202100224 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 06:09:16,108 resample.py get_mission_start_end():1145 [1] ctd1 : 2004-11-16T17:36:01.714945792 to 2004-11-16T22:38:24.302093568 (0 days 00:00:00 before mission_end) INFO 2025-06-26 06:09:16,109 resample.py get_mission_start_end():1145 [1] ctd2 : 2004-11-16T17:36:01.774941696 to 2004-11-16T22:38:24.152103936 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 06:09:16,111 resample.py get_mission_start_end():1145 [1] isus : 2004-11-16T17:36:42.712137472 to 2004-11-16T22:38:23.922119680 (0 days 00:00:00.379973888 before mission_end) INFO 2025-06-26 06:09:16,112 resample.py get_mission_start_end():1145 [1] biolume : 2004-11-16T17:35:40.746348160 to 2004-11-16T22:38:23.712099840 (0 days 00:00:00.589993728 before mission_end) INFO 2025-06-26 06:09:16,113 resample.py get_mission_start_end():1145 [1] tailcone : 2004-11-16T17:35:41.976298112 to 2004-11-16T22:38:24.192100992 (0 days 00:00:00.109992576 before mission_end) INFO 2025-06-26 06:09:16,114 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_align.nc mission netCDF file INFO 2025-06-26 06:09:16,115 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,315 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,351 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,385 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,420 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,451 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,481 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,511 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,541 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,569 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,597 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,624 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,652 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,680 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,707 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,734 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,762 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,791 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,821 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,850 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,879 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,909 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,938 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,953 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,967 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,982 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:16,999 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:17,037 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 06:09:17,238 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_1S.nc INFO 2025-06-26 06:09:18,327 create_products.py gulper_odv():401 [1] No gulper times found for 2004.321.00 INFO 2025-06-26 06:09:18,328 process.py archive():337 [1] Archiving steps for 2004.321.00 INFO 2025-06-26 06:09:18,328 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00, BASE_PATH = /data/auv_data INFO 2025-06-26 06:09:18,328 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00 files to /Volumes/AUVCTD/surveys/2004/netcdf INFO 2025-06-26 06:09:18,329 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.321.00_1S.nc INFO 2025-06-26 06:09:18,354 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_1S.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:09:18,354 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.321.00_cal.nc INFO 2025-06-26 06:09:18,447 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_cal.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:09:18,449 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2004/netcdf/dorado_2004.321.00_align.nc INFO 2025-06-26 06:09:18,545 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_align.nc /Volumes/AUVCTD/surveys/2004/netcdf done. INFO 2025-06-26 06:09:18,575 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,602 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,608 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,628 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,681 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,688 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,708 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,734 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,787 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2004/2004321/2004.321.00 done. INFO 2025-06-26 06:09:18,788 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 06:09:18,788 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2004.321.00/dorado_2004.321.00_processing.log /Volumes/AUVCTD/surveys/2004/netcdf