----------------------------------------------- NOVOPlasty: The Organelle Assembler Version 2.6.4 Author: Nicolas Dierckxsens, (c) 2015-2018 ----------------------------------------------- Input parameters from the configuration file: *** Verify if everything is correct *** Project: ----------------------- Project name = Hyalella_mtdna Type = mito Genome range = 12000-20000 K-mer = 39 Max memory = Extended log = 1 Save assembled reads = no Seed Input = Hyalella_COI.fasta Reference sequence = Variance detection = no Heteroplasmy = Chloroplast sequence = Dataset 1: ----------------------- Read Length = 101 Insert size = 132 Platform = illumina Single/Paired = PE Combined reads = Forward reads = SRR1556038_1.fastq Reverse reads = SRR1556038_2.fastq Optional: ----------------------- Insert size auto = yes Insert range = 1.8 Insert range strict = 1.3 Reading Input......OK Building Hash Table......OK Subsampled fraction: 10.83 % Retrieve Seed......OK Initial read retrieved successfully: TAGGTCTGAATTATTACTCGTTGACTATTTTCTACAAACCACAAGGATATTGGAACGCTGTATTTTATTTTAGGGGCTTGAGCTAGGGCGATCGGGACTTC Start Assembly... 101 bp assembled 101 bp assembled 126 bp assembled 154 bp assembled 202 bp assembled 252 bp assembled 297 bp assembled 346 bp assembled 398 bp assembled 435 bp assembled 489 bp assembled 528 bp assembled 580 bp assembled 626 bp assembled 671 bp assembled 708 bp assembled 758 bp assembled 808 bp assembled 855 bp assembled 898 bp assembled 935 bp assembled 986 bp assembled 1039 bp assembled 1076 bp assembled 1127 bp assembled 1180 bp assembled 1210 bp assembled 1269 bp assembled 1307 bp assembled 1343 bp assembled 1396 bp assembled 1448 bp assembled 1487 bp assembled 1536 bp assembled 1571 bp assembled 1627 bp assembled 1670 bp assembled 1726 bp assembled 1772 bp assembled 1820 bp assembled 1864 bp assembled 1911 bp assembled 1956 bp assembled 2003 bp assembled 2055 bp assembled 2109 bp assembled 2150 bp assembled 2205 bp assembled 2238 bp assembled 2282 bp assembled 2333 bp assembled 2382 bp assembled 2432 bp assembled 2474 bp assembled 2509 bp assembled 2533 bp assembled 2561 bp assembled 2589 bp assembled 2613 bp assembled 2658 bp assembled 2680 bp assembled 2697 bp assembled 2718 bp assembled 2761 bp assembled 2781 bp assembled 2822 bp assembled 2844 bp assembled 2886 bp assembled 2904 bp assembled 2955 bp assembled 2976 bp assembled 3043 bp assembled 3081 bp assembled 3136 bp assembled 3192 bp assembled 3235 bp assembled 3281 bp assembled 3319 bp assembled 3348 bp assembled 3375 bp assembled 3395 bp assembled 3415 bp assembled 3448 bp assembled 3477 bp assembled 3497 bp assembled 3570 bp assembled 3630 bp assembled 3679 bp assembled 3727 bp assembled 3770 bp assembled 3817 bp assembled 3864 bp assembled 3901 bp assembled 3925 bp assembled 3956 bp assembled 3978 bp assembled 4009 bp assembled 4029 bp assembled 4083 bp assembled 4145 bp assembled 4180 bp assembled 4222 bp assembled 4275 bp assembled 4318 bp assembled 4375 bp assembled 4424 bp assembled 4473 bp assembled 4525 bp assembled 4573 bp assembled 4614 bp assembled 4667 bp assembled 4711 bp assembled 4753 bp assembled 4802 bp assembled 4849 bp assembled 4891 bp assembled 4949 bp assembled 4991 bp assembled 5035 bp assembled 5081 bp assembled 5126 bp assembled 5168 bp assembled 5227 bp assembled 5267 bp assembled 5312 bp assembled 5366 bp assembled 5409 bp assembled 5457 bp assembled 5505 bp assembled 5548 bp assembled 5598 bp assembled 5645 bp assembled 5690 bp assembled 5740 bp assembled 5791 bp assembled 5834 bp assembled 5881 bp assembled 5932 bp assembled 5974 bp assembled 6013 bp assembled 6064 bp assembled 6113 bp assembled 6161 bp assembled 6217 bp assembled 6257 bp assembled 6296 bp assembled 6346 bp assembled 6390 bp assembled 6441 bp assembled 6493 bp assembled 6539 bp assembled 6577 bp assembled 6623 bp assembled 6668 bp assembled 6718 bp assembled 6766 bp assembled 6816 bp assembled 6861 bp assembled 6899 bp assembled 6949 bp assembled 6994 bp assembled 7038 bp assembled 7087 bp assembled 7137 bp assembled 7185 bp assembled 7221 bp assembled 7266 bp assembled 7319 bp assembled 7362 bp assembled 7413 bp assembled 7462 bp assembled 7513 bp assembled 7555 bp assembled 7603 bp assembled 7646 bp assembled 7695 bp assembled 7736 bp assembled 7781 bp assembled 7836 bp assembled 7884 bp assembled 7930 bp assembled 7974 bp assembled 8023 bp assembled 8065 bp assembled 8110 bp assembled 8160 bp assembled 8204 bp assembled 8255 bp assembled 8305 bp assembled 8359 bp assembled 8394 bp assembled 8434 bp assembled 8473 bp assembled 8519 bp assembled 8568 bp assembled 8623 bp assembled 8674 bp assembled 8707 bp assembled 8751 bp assembled 8801 bp assembled 8843 bp assembled 8880 bp assembled 8923 bp assembled 8966 bp assembled 9021 bp assembled 9072 bp assembled 9121 bp assembled 9170 bp assembled 9218 bp assembled 9264 bp assembled 9305 bp assembled 9348 bp assembled 9405 bp assembled 9441 bp assembled 9498 bp assembled 9542 bp assembled 9599 bp assembled 9634 bp assembled 9680 bp assembled 9729 bp assembled 9769 bp assembled 9817 bp assembled 9865 bp assembled 9906 bp assembled 9958 bp assembled 9999 bp assembled 10043 bp assembled 10094 bp assembled 10147 bp assembled 10196 bp assembled 10238 bp assembled 10267 bp assembled 10318 bp assembled 10371 bp assembled 10408 bp assembled 10458 bp assembled 10504 bp assembled 10555 bp assembled 10599 bp assembled 10647 bp assembled 10690 bp assembled 10725 bp assembled 10774 bp assembled 10816 bp assembled 10866 bp assembled 10908 bp assembled 10963 bp assembled 11016 bp assembled 11061 bp assembled 11113 bp assembled 11150 bp assembled 11196 bp assembled 11238 bp assembled 11287 bp assembled 11330 bp assembled 11377 bp assembled 11427 bp assembled 11475 bp assembled 11513 bp assembled 11555 bp assembled 11603 bp assembled 11653 bp assembled 11696 bp assembled 11748 bp assembled 11803 bp assembled 11847 bp assembled 11884 bp assembled 11930 bp assembled 11978 bp assembled 12031 bp assembled 12074 bp assembled 12113 bp assembled 12154 bp assembled 12207 bp assembled 12258 bp assembled 12301 bp assembled 12340 bp assembled 12358 bp assembled 12375 bp assembled 12403 bp assembled 12427 bp assembled 12452 bp assembled 12497 bp assembled 12520 bp assembled 12547 bp assembled 12568 bp assembled 12588 bp assembled 12614 bp assembled 12644 bp assembled 12659 bp assembled 12687 bp assembled 12709 bp assembled 12737 bp assembled 12755 bp assembled 12784 bp assembled 12811 bp assembled 12826 bp assembled 12840 bp assembled 12846 bp assembled 12852 bp assembled 12859 bp assembled 12865 bp assembled 12894 bp assembled 12934 bp assembled 12952 bp assembled 12983 bp assembled 13007 bp assembled 13028 bp assembled 13051 bp assembled 13075 bp assembled 13097 bp assembled 13120 bp assembled 13154 bp assembled 13175 bp assembled 13201 bp assembled 13223 bp assembled 13250 bp assembled 13277 bp assembled 13293 bp assembled 13313 bp assembled 13334 bp assembled 13359 bp assembled 13384 bp assembled 13410 bp assembled 13436 bp assembled 13451 bp assembled 13473 bp assembled 13500 bp assembled 13527 bp assembled 13543 bp assembled 13561 bp assembled 13593 bp assembled 13609 bp assembled 13633 bp assembled 13658 bp assembled 13683 bp assembled 13706 bp assembled 13731 bp assembled 13753 bp assembled 13774 bp assembled 13798 bp assembled 13820 bp assembled 13842 bp assembled 13871 bp assembled 13893 bp assembled 13912 bp assembled 13927 bp assembled 13954 bp assembled 13979 bp assembled 14001 bp assembled 14027 bp assembled 14053 bp assembled 14072 bp assembled 14095 bp assembled 14119 bp assembled 14143 bp assembled 14168 bp assembled 14190 bp assembled 14218 bp assembled 14240 bp assembled 14269 bp assembled 14287 bp assembled 14305 bp assembled 14327 bp assembled 14348 bp assembled 14376 bp assembled 14402 bp assembled 14426 bp assembled 14449 bp assembled 14469 bp assembled 14495 bp assembled 14519 bp assembled 14542 bp assembled 14561 bp assembled 14581 bp assembled 14601 bp assembled 14632 bp assembled 14661 bp assembled 14679 bp assembled 14709 bp assembled 14727 bp assembled 14753 bp assembled 14774 bp assembled 14806 bp assembled 14823 bp assembled 14849 bp assembled 14876 bp assembled 14908 bp assembled 14924 bp assembled 14951 bp assembled 14973 bp assembled 14994 bp assembled 15020 bp assembled 15040 bp assembled 15063 bp assembled 15084 bp assembled 15115 bp assembled 15131 bp assembled 15159 bp assembled 15189 bp assembled 15207 bp assembled 15224 bp assembled 15246 bp assembled 15274 bp assembled 15299 bp assembled 15327 bp assembled 15345 bp assembled 15375 bp assembled 15396 bp assembled 15418 bp assembled 15443 bp assembled 15463 bp assembled 15489 bp assembled 15511 bp assembled 15535 bp assembled 15563 bp assembled 15586 bp assembled 15609 bp assembled 15634 bp assembled 15657 bp assembled 15681 bp assembled 15715 bp assembled 15730 bp assembled 15748 bp assembled 15768 bp assembled 15795 bp assembled 15817 bp assembled 15837 bp assembled 15872 bp assembled 15893 bp assembled 15912 bp assembled 15938 bp assembled 15957 bp assembled 15965 bp assembled 15977 bp assembled 15989 bp assembled 15997 bp assembled 16001 bp assembled 16001 bp assembled 16001 bp assembled 16045 bp assembled 16045 bp assembled 16045 bp assembled 16078 bp assembled 16107 bp assembled 16133 bp assembled 16158 bp assembled 16184 bp assembled 16204 bp assembled 16230 bp assembled 16256 bp assembled 16281 bp assembled 16310 bp assembled 16336 bp assembled 16360 bp assembled 16381 bp assembled 16403 bp assembled 16423 bp assembled 16449 bp assembled 16477 bp assembled 16494 bp assembled 16522 bp assembled 16543 bp assembled 16568 bp assembled 16590 bp assembled 16616 bp assembled 16639 bp assembled 16662 bp assembled 16683 bp assembled 16714 bp assembled 16735 bp assembled 16756 bp assembled 16778 bp assembled 16801 bp assembled 16829 bp assembled 16853 bp assembled 16876 bp assembled 16896 bp assembled 16919 bp assembled 16942 bp assembled 16970 bp assembled 16990 bp assembled 17017 bp assembled 17037 bp assembled 17061 bp assembled 17077 bp assembled 17107 bp assembled 17128 bp assembled 17153 bp assembled 17171 bp assembled 17201 bp assembled 17222 bp assembled 17253 bp assembled 17270 bp assembled 17292 bp assembled 17321 bp assembled 17343 bp assembled 17370 bp assembled 17394 bp assembled 17419 bp assembled 17439 bp assembled 17461 bp assembled 17486 bp assembled 17512 bp assembled 17539 bp assembled 17559 bp assembled 17578 bp assembled 17592 bp assembled 17627 bp assembled 17646 bp assembled 17664 bp assembled 17693 bp assembled 17712 bp assembled 17737 bp assembled 17763 bp assembled 17787 bp assembled 17811 bp assembled 17834 bp assembled 17860 bp assembled 17879 bp assembled 17906 bp assembled 17925 bp assembled 17950 bp assembled 17970 bp assembled 18003 bp assembled 18024 bp assembled 18043 bp assembled 18066 bp assembled 18088 bp assembled 18112 bp assembled 18138 bp assembled 18165 bp assembled 18184 bp assembled 18209 bp assembled 18229 bp assembled 18249 bp assembled 18279 bp assembled 18303 bp assembled 18331 bp assembled 18362 bp assembled 18381 bp assembled 18390 bp assembled 18420 bp assembled 18442 bp assembled 18468 bp assembled 18493 bp assembled 18513 bp assembled 18541 bp assembled 18568 bp assembled 18586 bp assembled 18609 bp assembled 18639 bp assembled 18657 bp assembled 18673 bp assembled 18699 bp assembled 18719 bp assembled 18743 bp assembled 18771 bp assembled 18793 bp assembled 18823 bp assembled 18840 bp assembled 18860 bp assembled 18890 bp assembled 18908 bp assembled 18933 bp assembled 18950 bp assembled 18978 bp assembled 18997 bp assembled 19031 bp assembled 19054 bp assembled 19078 bp assembled 19097 bp assembled 19122 bp assembled 19141 bp assembled 19162 bp assembled 19180 bp assembled 19200 bp assembled 19239 bp assembled 19264 bp assembled 19285 bp assembled 19309 bp assembled 19332 bp assembled 19361 bp assembled 19378 bp assembled 19405 bp assembled 19432 bp assembled 19453 bp assembled 19478 bp assembled 19504 bp assembled 19524 bp assembled 19545 bp assembled 19571 bp assembled 19595 bp assembled 19621 bp assembled 19641 bp assembled 19662 bp assembled 19691 bp assembled 19715 bp assembled 19740 bp assembled 19758 bp assembled 19781 bp assembled 19808 bp assembled 19835 bp assembled 19860 bp assembled 19887 bp assembled 19903 bp assembled 19922 bp assembled 19945 bp assembled 19970 bp assembled 19997 bp assembled  ------------Assembly 1 finished: Contigs are automatically merged in Merged_contigs file------------ Contig 01 : 20018 bp Total contigs : 1 Largest contig : 20018 bp Smallest contig : 20018 bp Average insert size : 153 bp -----------------------------------------Input data metrics----------------------------------------- Total reads : 26088796 Aligned reads : 78224 Assembled reads : 35242 Average organelle coverage : 395 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Command being timed: "/app/redhat6/NOVOPlasty/NOVOPlasty-master/NOVOPlasty2.6.5.pl -c config.txt" User time (seconds): 719.54 System time (seconds): 40.67 Percent of CPU this job got: 99% Elapsed (wall clock) time (h:mm:ss or m:ss): 12:41.73 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 Maximum resident set size (kbytes): 54537440 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 2856389 Voluntary context switches: 4427 Involuntary context switches: 142786 Swaps: 0 File system inputs: 0 File system outputs: 0 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 Page size (bytes): 4096 Exit status: 0