Getting short reads.
Getting assembly.
command: bwa index /kb/module/work/tmp/GV048_filtlong_flye.contigs.fa
[bwa_index] Pack FASTA... 0.06 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 2.68 seconds elapse.
[bwa_index] Update BWT... 0.05 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.74 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /kb/module/work/tmp/GV048_filtlong_flye.contigs.fa
[main] Real time: 3.574 sec; CPU: 3.570 sec
command: bwa mem -a -k1 -T7 -A1 -B1 -O1 -E1 -L100 /kb/module/work/tmp/GV048_filtlong_flye.contigs.fa /kb/module/work/tmp/a9fdd887-3447-4f1d-a99c-df1c04aa7bbc.single.fastq > /kb/module/work/tmp/alignments1_c82f3c2a-411d-4680-9a4c-1857e0913429.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2592 sequences (10018680 bp)...
[M::process] read 2740 sequences (10001602 bp)...
[M::mem_process_seqs] Processed 2592 reads in 46.425 CPU sec, 46.388 real sec
[M::process] read 2706 sequences (10004287 bp)...
[M::mem_process_seqs] Processed 2740 reads in 44.743 CPU sec, 44.653 real sec
[M::process] read 2586 sequences (10002730 bp)...
[M::mem_process_seqs] Processed 2706 reads in 45.855 CPU sec, 45.758 real sec
[M::process] read 2628 sequences (10006902 bp)...
[M::mem_process_seqs] Processed 2586 reads in 44.963 CPU sec, 44.870 real sec
[M::process] read 2582 sequences (10021385 bp)...
[M::mem_process_seqs] Processed 2628 reads in 47.997 CPU sec, 47.908 real sec
[M::process] read 2610 sequences (10000710 bp)...
[M::mem_process_seqs] Processed 2582 reads in 46.621 CPU sec, 46.531 real sec
[M::process] read 2514 sequences (10003160 bp)...
[M::mem_process_seqs] Processed 2610 reads in 48.734 CPU sec, 48.639 real sec
[M::process] read 2446 sequences (10004463 bp)...
[M::mem_process_seqs] Processed 2514 reads in 48.364 CPU sec, 48.283 real sec
[M::process] read 2716 sequences (10001558 bp)...
[M::mem_process_seqs] Processed 2446 reads in 104.484 CPU sec, 104.398 real sec
[M::process] read 2646 sequences (10010812 bp)...
[M::mem_process_seqs] Processed 2716 reads in 43.721 CPU sec, 43.640 real sec
[M::process] read 2592 sequences (10000282 bp)...
[M::mem_process_seqs] Processed 2646 reads in 46.363 CPU sec, 46.272 real sec
[M::process] read 2660 sequences (10001721 bp)...
[M::mem_process_seqs] Processed 2592 reads in 45.734 CPU sec, 45.637 real sec
[M::process] read 2642 sequences (10008472 bp)...
[M::mem_process_seqs] Processed 2660 reads in 47.829 CPU sec, 47.733 real sec
[M::process] read 2560 sequences (10001531 bp)...
[M::mem_process_seqs] Processed 2642 reads in 45.934 CPU sec, 45.856 real sec
[M::process] read 2630 sequences (10009953 bp)...
[M::mem_process_seqs] Processed 2560 reads in 44.277 CPU sec, 44.178 real sec
[M::process] read 2714 sequences (10004973 bp)...
[M::mem_process_seqs] Processed 2630 reads in 44.697 CPU sec, 44.607 real sec
[M::process] read 2718 sequences (10002965 bp)...
[M::mem_process_seqs] Processed 2714 reads in 42.207 CPU sec, 42.128 real sec
[M::process] read 2744 sequences (10013513 bp)...
[M::mem_process_seqs] Processed 2718 reads in 43.138 CPU sec, 43.043 real sec
[M::process] read 2968 sequences (10019325 bp)...
[M::mem_process_seqs] Processed 2744 reads in 44.245 CPU sec, 44.152 real sec
[M::process] read 2862 sequences (10032526 bp)...
[M::mem_process_seqs] Processed 2968 reads in 42.027 CPU sec, 41.947 real sec
[M::process] read 2606 sequences (10003571 bp)...
[M::mem_process_seqs] Processed 2862 reads in 43.661 CPU sec, 43.566 real sec
[M::process] read 2608 sequences (10001436 bp)...
[M::mem_process_seqs] Processed 2606 reads in 44.745 CPU sec, 44.664 real sec
[M::process] read 2654 sequences (10004729 bp)...
[M::mem_process_seqs] Processed 2608 reads in 44.194 CPU sec, 44.103 real sec
[M::process] read 2612 sequences (10010027 bp)...
[M::mem_process_seqs] Processed 2654 reads in 43.036 CPU sec, 42.944 real sec
[M::process] read 2628 sequences (10000361 bp)...
[M::mem_process_seqs] Processed 2612 reads in 43.520 CPU sec, 43.429 real sec
[M::process] read 2638 sequences (10001765 bp)...
[M::mem_process_seqs] Processed 2628 reads in 46.093 CPU sec, 46.014 real sec
[M::process] read 2514 sequences (10010427 bp)...
[M::mem_process_seqs] Processed 2638 reads in 45.758 CPU sec, 45.660 real sec
[M::process] read 2754 sequences (10003058 bp)...
[M::mem_process_seqs] Processed 2514 reads in 46.260 CPU sec, 46.178 real sec
[M::process] read 2800 sequences (10000142 bp)...
[M::mem_process_seqs] Processed 2754 reads in 45.180 CPU sec, 45.085 real sec
[M::process] read 2718 sequences (10010607 bp)...
[M::mem_process_seqs] Processed 2800 reads in 42.433 CPU sec, 42.339 real sec
[M::process] read 2662 sequences (10000613 bp)...
[M::mem_process_seqs] Processed 2718 reads in 43.500 CPU sec, 43.417 real sec
[M::process] read 2678 sequences (10007337 bp)...
[M::mem_process_seqs] Processed 2662 reads in 47.170 CPU sec, 47.077 real sec
[M::process] read 2720 sequences (10014227 bp)...
[M::mem_process_seqs] Processed 2678 reads in 43.509 CPU sec, 43.430 real sec
[M::process] read 2548 sequences (10003188 bp)...
[M::mem_process_seqs] Processed 2720 reads in 45.269 CPU sec, 45.193 real sec
[M::process] read 2786 sequences (10012125 bp)...
[M::mem_process_seqs] Processed 2548 reads in 46.269 CPU sec, 46.175 real sec
[M::process] read 2572 sequences (10001836 bp)...
[M::mem_process_seqs] Processed 2786 reads in 42.686 CPU sec, 42.608 real sec
[M::process] read 2738 sequences (10003840 bp)...
[M::mem_process_seqs] Processed 2572 reads in 45.911 CPU sec, 45.830 real sec
[M::process] read 2610 sequences (10065941 bp)...
[M::mem_process_seqs] Processed 2738 reads in 43.737 CPU sec, 43.626 real sec
[M::process] read 2652 sequences (10000610 bp)...
[M::mem_process_seqs] Processed 2610 reads in 46.679 CPU sec, 46.590 real sec
[M::process] read 2468 sequences (10002938 bp)...
[M::mem_process_seqs] Processed 2652 reads in 48.386 CPU sec, 48.296 real sec
[M::process] read 2622 sequences (10005685 bp)...
[M::mem_process_seqs] Processed 2468 reads in 46.307 CPU sec, 46.215 real sec
[M::process] read 2626 sequences (10012052 bp)...
[M::mem_process_seqs] Processed 2622 reads in 44.112 CPU sec, 44.015 real sec
[M::process] read 2626 sequences (10002582 bp)...
[M::mem_process_seqs] Processed 2626 reads in 43.711 CPU sec, 43.614 real sec
[M::process] read 2858 sequences (10002094 bp)...
[M::mem_process_seqs] Processed 2626 reads in 46.933 CPU sec, 46.854 real sec
[M::process] read 2776 sequences (10004932 bp)...
[M::mem_process_seqs] Processed 2858 reads in 43.555 CPU sec, 43.458 real sec
[M::process] read 2806 sequences (10001681 bp)...
[M::mem_process_seqs] Processed 2776 reads in 44.442 CPU sec, 44.348 real sec
[M::process] read 2718 sequences (10007929 bp)...
[M::mem_process_seqs] Processed 2806 reads in 40.389 CPU sec, 40.300 real sec
[M::process] read 2660 sequences (10006075 bp)...
[M::mem_process_seqs] Processed 2718 reads in 44.279 CPU sec, 44.187 real sec
[M::process] read 2680 sequences (10010873 bp)...
[M::mem_process_seqs] Processed 2660 reads in 45.904 CPU sec, 45.808 real sec
[M::process] read 2794 sequences (10006834 bp)...
[M::mem_process_seqs] Processed 2680 reads in 43.764 CPU sec, 43.691 real sec
[M::process] read 3090 sequences (10008398 bp)...
[M::mem_process_seqs] Processed 2794 reads in 46.680 CPU sec, 46.588 real sec
[M::process] read 2894 sequences (10005731 bp)...
[M::mem_process_seqs] Processed 3090 reads in 42.812 CPU sec, 42.721 real sec
[M::process] read 2466 sequences (10008237 bp)...
[M::mem_process_seqs] Processed 2894 reads in 44.879 CPU sec, 44.802 real sec
[M::process] read 2678 sequences (10009648 bp)...
[M::mem_process_seqs] Processed 2466 reads in 48.327 CPU sec, 48.234 real sec
[M::process] read 2684 sequences (10009938 bp)...
[M::mem_process_seqs] Processed 2678 reads in 45.370 CPU sec, 45.279 real sec
[M::process] read 2626 sequences (10004595 bp)...
[M::mem_process_seqs] Processed 2684 reads in 46.249 CPU sec, 46.164 real sec
[M::process] read 2712 sequences (10006401 bp)...
[M::mem_process_seqs] Processed 2626 reads in 46.131 CPU sec, 46.054 real sec
[M::process] read 2706 sequences (10002260 bp)...
[M::mem_process_seqs] Processed 2712 reads in 45.245 CPU sec, 45.165 real sec
[M::process] read 2622 sequences (10000003 bp)...
[M::mem_process_seqs] Processed 2706 reads in 45.665 CPU sec, 45.575 real sec
[M::process] read 2634 sequences (10017476 bp)...
[M::mem_process_seqs] Processed 2622 reads in 48.394 CPU sec, 48.307 real sec
[M::process] read 2798 sequences (10026040 bp)...
[M::mem_process_seqs] Processed 2634 reads in 46.736 CPU sec, 46.657 real sec
[M::process] read 2764 sequences (10001352 bp)...
[M::mem_process_seqs] Processed 2798 reads in 41.889 CPU sec, 41.811 real sec
[M::process] read 2666 sequences (10017612 bp)...
[M::mem_process_seqs] Processed 2764 reads in 42.989 CPU sec, 42.894 real sec
[M::process] read 2650 sequences (10005584 bp)...
[M::mem_process_seqs] Processed 2666 reads in 45.043 CPU sec, 44.953 real sec
[M::process] read 2574 sequences (10017162 bp)...
[M::mem_process_seqs] Processed 2650 reads in 44.627 CPU sec, 44.533 real sec
[M::process] read 2606 sequences (10003062 bp)...
[M::mem_process_seqs] Processed 2574 reads in 45.485 CPU sec, 45.394 real sec
[M::process] read 2722 sequences (10000099 bp)...
[M::mem_process_seqs] Processed 2606 reads in 45.819 CPU sec, 45.729 real sec
[M::process] read 2708 sequences (10006939 bp)...
[M::mem_process_seqs] Processed 2722 reads in 44.636 CPU sec, 44.554 real sec
[M::process] read 2686 sequences (10001034 bp)...
[M::mem_process_seqs] Processed 2708 reads in 49.160 CPU sec, 49.068 real sec
[M::process] read 2874 sequences (10003000 bp)...
[M::mem_process_seqs] Processed 2686 reads in 45.952 CPU sec, 45.858 real sec
[M::process] read 3160 sequences (10003218 bp)...
[M::mem_process_seqs] Processed 2874 reads in 44.896 CPU sec, 44.814 real sec
[M::process] read 2958 sequences (10009564 bp)...
[M::mem_process_seqs] Processed 3160 reads in 41.546 CPU sec, 41.454 real sec
[M::process] read 2772 sequences (10000485 bp)...
[M::mem_process_seqs] Processed 2958 reads in 42.065 CPU sec, 41.971 real sec
[M::process] read 2614 sequences (10006090 bp)...
[M::mem_process_seqs] Processed 2772 reads in 44.529 CPU sec, 44.435 real sec
[M::process] read 2750 sequences (10004912 bp)...
[M::mem_process_seqs] Processed 2614 reads in 42.764 CPU sec, 42.672 real sec
[M::process] read 2702 sequences (10001269 bp)...
[M::mem_process_seqs] Processed 2750 reads in 42.400 CPU sec, 42.293 real sec
[M::process] read 2852 sequences (10002784 bp)...
[M::mem_process_seqs] Processed 2702 reads in 43.464 CPU sec, 43.368 real sec
[M::process] read 2840 sequences (10009604 bp)...
[M::mem_process_seqs] Processed 2852 reads in 46.823 CPU sec, 46.731 real sec
[M::process] read 2774 sequences (10004008 bp)...
[M::mem_process_seqs] Processed 2840 reads in 46.750 CPU sec, 46.668 real sec
[M::process] read 2818 sequences (10012571 bp)...
[M::mem_process_seqs] Processed 2774 reads in 46.238 CPU sec, 46.163 real sec
[M::process] read 2858 sequences (10013043 bp)...
[M::mem_process_seqs] Processed 2818 reads in 46.496 CPU sec, 46.403 real sec
[M::process] read 2732 sequences (10005882 bp)...
[M::mem_process_seqs] Processed 2858 reads in 44.471 CPU sec, 44.381 real sec
[M::process] read 2732 sequences (10007131 bp)...
[M::mem_process_seqs] Processed 2732 reads in 47.629 CPU sec, 47.538 real sec
[M::process] read 2556 sequences (10004691 bp)...
[M::mem_process_seqs] Processed 2732 reads in 48.671 CPU sec, 48.593 real sec
[M::process] read 2656 sequences (10000724 bp)...
[M::mem_process_seqs] Processed 2556 reads in 49.740 CPU sec, 49.651 real sec
[M::process] read 2706 sequences (10004870 bp)...
[M::mem_process_seqs] Processed 2656 reads in 48.029 CPU sec, 47.950 real sec
[M::process] read 2554 sequences (10001337 bp)...
[M::mem_process_seqs] Processed 2706 reads in 44.771 CPU sec, 44.678 real sec
[M::process] read 2790 sequences (10000058 bp)...
[M::mem_process_seqs] Processed 2554 reads in 46.729 CPU sec, 46.638 real sec
[M::process] read 2744 sequences (10002544 bp)...
[M::mem_process_seqs] Processed 2790 reads in 45.418 CPU sec, 45.327 real sec
[M::process] read 2554 sequences (10002678 bp)...
[M::mem_process_seqs] Processed 2744 reads in 46.473 CPU sec, 46.382 real sec
[M::process] read 2656 sequences (10023696 bp)...
[M::mem_process_seqs] Processed 2554 reads in 48.292 CPU sec, 48.206 real sec
[M::process] read 2568 sequences (10002023 bp)...
[M::mem_process_seqs] Processed 2656 reads in 48.143 CPU sec, 48.047 real sec
[M::process] read 2632 sequences (10001712 bp)...
[M::mem_process_seqs] Processed 2568 reads in 44.886 CPU sec, 44.803 real sec
[M::process] read 2656 sequences (10012284 bp)...
[M::mem_process_seqs] Processed 2632 reads in 44.426 CPU sec, 44.343 real sec
[M::process] read 2922 sequences (10002712 bp)...
[M::mem_process_seqs] Processed 2656 reads in 43.730 CPU sec, 43.661 real sec
[M::process] read 2696 sequences (10005349 bp)...
[M::mem_process_seqs] Processed 2922 reads in 42.019 CPU sec, 41.961 real sec
[M::process] read 2578 sequences (10015168 bp)...
[M::mem_process_seqs] Processed 2696 reads in 43.357 CPU sec, 43.300 real sec
[M::process] read 2620 sequences (10002441 bp)...
[M::mem_process_seqs] Processed 2578 reads in 45.974 CPU sec, 45.918 real sec
[M::process] read 2636 sequences (10002014 bp)...
[M::mem_process_seqs] Processed 2620 reads in 46.570 CPU sec, 46.512 real sec
[M::process] read 2508 sequences (10034543 bp)...
[M::mem_process_seqs] Processed 2636 reads in 43.789 CPU sec, 43.726 real sec
[M::process] read 2604 sequences (10010631 bp)...
[M::mem_process_seqs] Processed 2508 reads in 44.015 CPU sec, 43.959 real sec
[M::process] read 2612 sequences (10000865 bp)...
[M::mem_process_seqs] Processed 2604 reads in 44.398 CPU sec, 44.332 real sec
[M::process] read 2820 sequences (10002664 bp)...
[M::mem_process_seqs] Processed 2612 reads in 45.739 CPU sec, 45.657 real sec
[M::process] read 2962 sequences (10014419 bp)...
[M::mem_process_seqs] Processed 2820 reads in 43.618 CPU sec, 43.535 real sec
[M::process] read 2766 sequences (10008756 bp)...
[M::mem_process_seqs] Processed 2962 reads in 41.471 CPU sec, 41.379 real sec
[M::process] read 2690 sequences (10007888 bp)...
[M::mem_process_seqs] Processed 2766 reads in 43.769 CPU sec, 43.687 real sec
[M::process] read 2698 sequences (10001205 bp)...
[M::mem_process_seqs] Processed 2690 reads in 44.151 CPU sec, 44.104 real sec
[M::process] read 2558 sequences (10000695 bp)...
[M::mem_process_seqs] Processed 2698 reads in 44.080 CPU sec, 43.987 real sec
[M::process] read 2536 sequences (10001631 bp)...
[M::mem_process_seqs] Processed 2558 reads in 45.775 CPU sec, 45.685 real sec
[M::process] read 2690 sequences (10005923 bp)...
[M::mem_process_seqs] Processed 2536 reads in 45.531 CPU sec, 45.431 real sec
[M::process] read 2738 sequences (10009838 bp)...
[M::mem_process_seqs] Processed 2690 reads in 43.717 CPU sec, 43.622 real sec
[M::process] read 2612 sequences (10004771 bp)...
[M::mem_process_seqs] Processed 2738 reads in 44.427 CPU sec, 44.336 real sec
[M::process] read 2592 sequences (10001489 bp)...
[M::mem_process_seqs] Processed 2612 reads in 46.489 CPU sec, 46.402 real sec
[M::process] read 2698 sequences (10000838 bp)...
[M::mem_process_seqs] Processed 2592 reads in 46.932 CPU sec, 46.831 real sec
[M::process] read 2924 sequences (10001143 bp)...
[M::mem_process_seqs] Processed 2698 reads in 43.663 CPU sec, 43.615 real sec
[M::process] read 3144 sequences (10003512 bp)...
[M::mem_process_seqs] Processed 2924 reads in 43.117 CPU sec, 43.024 real sec
[M::process] read 2622 sequences (10012580 bp)...
[M::mem_process_seqs] Processed 3144 reads in 40.272 CPU sec, 40.180 real sec
[M::process] read 2642 sequences (10005809 bp)...
[M::mem_process_seqs] Processed 2622 reads in 44.679 CPU sec, 44.599 real sec
[M::process] read 2928 sequences (10002075 bp)...
[M::mem_process_seqs] Processed 2642 reads in 45.831 CPU sec, 45.741 real sec
[M::process] read 3044 sequences (10002551 bp)...
[M::mem_process_seqs] Processed 2928 reads in 41.367 CPU sec, 41.268 real sec
[M::process] read 2610 sequences (10011238 bp)...
[M::mem_process_seqs] Processed 3044 reads in 42.032 CPU sec, 41.950 real sec
[M::process] read 2858 sequences (10004481 bp)...
[M::mem_process_seqs] Processed 2610 reads in 44.133 CPU sec, 44.046 real sec
[M::process] read 2898 sequences (10004160 bp)...
[M::mem_process_seqs] Processed 2858 reads in 43.454 CPU sec, 43.360 real sec
[M::process] read 2846 sequences (10001206 bp)...
[M::mem_process_seqs] Processed 2898 reads in 41.859 CPU sec, 41.802 real sec
[M::process] read 2702 sequences (10002544 bp)...
[M::mem_process_seqs] Processed 2846 reads in 44.312 CPU sec, 44.219 real sec
[M::process] read 2824 sequences (10000298 bp)...
[M::mem_process_seqs] Processed 2702 reads in 43.769 CPU sec, 43.704 real sec
[M::process] read 2778 sequences (10022877 bp)...
[M::mem_process_seqs] Processed 2824 reads in 42.910 CPU sec, 42.817 real sec
[M::process] read 2640 sequences (10002964 bp)...
[M::mem_process_seqs] Processed 2778 reads in 42.406 CPU sec, 42.319 real sec
[M::process] read 3054 sequences (10013227 bp)...
[M::mem_process_seqs] Processed 2640 reads in 45.021 CPU sec, 44.931 real sec
[M::process] read 2988 sequences (10003704 bp)...
[M::mem_process_seqs] Processed 3054 reads in 44.979 CPU sec, 44.892 real sec
[M::process] read 2618 sequences (10000661 bp)...
[M::mem_process_seqs] Processed 2988 reads in 44.946 CPU sec, 44.879 real sec
[M::process] read 2548 sequences (10004816 bp)...
[M::mem_process_seqs] Processed 2618 reads in 47.938 CPU sec, 47.849 real sec
[M::process] read 2640 sequences (10013619 bp)...
[M::mem_process_seqs] Processed 2548 reads in 46.635 CPU sec, 46.558 real sec
[M::process] read 2530 sequences (10004104 bp)...
[M::mem_process_seqs] Processed 2640 reads in 45.620 CPU sec, 45.528 real sec
[M::process] read 2698 sequences (10022296 bp)...
[M::mem_process_seqs] Processed 2530 reads in 45.005 CPU sec, 44.909 real sec
[M::process] read 2880 sequences (10011198 bp)...
[M::mem_process_seqs] Processed 2698 reads in 43.110 CPU sec, 43.011 real sec
[M::process] read 2632 sequences (10000916 bp)...
[M::mem_process_seqs] Processed 2880 reads in 45.503 CPU sec, 45.423 real sec
[M::process] read 2838 sequences (10002698 bp)...
[M::mem_process_seqs] Processed 2632 reads in 46.585 CPU sec, 46.488 real sec
[M::process] read 2912 sequences (10000782 bp)...
[M::mem_process_seqs] Processed 2838 reads in 44.548 CPU sec, 44.458 real sec
[M::process] read 2786 sequences (10000445 bp)...
[M::mem_process_seqs] Processed 2912 reads in 43.199 CPU sec, 43.108 real sec
[M::process] read 2564 sequences (10008020 bp)...
[M::mem_process_seqs] Processed 2786 reads in 46.112 CPU sec, 46.019 real sec
[M::process] read 2690 sequences (10005535 bp)...
[M::mem_process_seqs] Processed 2564 reads in 46.024 CPU sec, 45.927 real sec
[M::process] read 2708 sequences (10001329 bp)...
[M::mem_process_seqs] Processed 2690 reads in 44.553 CPU sec, 44.457 real sec
[M::process] read 2898 sequences (10000237 bp)...
[M::mem_process_seqs] Processed 2708 reads in 47.166 CPU sec, 47.078 real sec
[M::process] read 2854 sequences (10002522 bp)...
[M::mem_process_seqs] Processed 2898 reads in 42.532 CPU sec, 42.444 real sec
[M::process] read 2974 sequences (10004534 bp)...
[M::mem_process_seqs] Processed 2854 reads in 44.973 CPU sec, 44.877 real sec
[M::process] read 2744 sequences (10006419 bp)...
[M::mem_process_seqs] Processed 2974 reads in 42.500 CPU sec, 42.406 real sec
[M::process] read 2664 sequences (10003556 bp)...
[M::mem_process_seqs] Processed 2744 reads in 43.200 CPU sec, 43.137 real sec
[M::process] read 2710 sequences (10004076 bp)...
[M::mem_process_seqs] Processed 2664 reads in 46.702 CPU sec, 46.611 real sec
[M::process] read 2608 sequences (10019258 bp)...
[M::mem_process_seqs] Processed 2710 reads in 45.302 CPU sec, 45.211 real sec
[M::process] read 2774 sequences (10001445 bp)...
[M::mem_process_seqs] Processed 2608 reads in 45.313 CPU sec, 45.222 real sec
[M::process] read 2804 sequences (10005072 bp)...
[M::mem_process_seqs] Processed 2774 reads in 42.376 CPU sec, 42.277 real sec
[M::process] read 2722 sequences (10001030 bp)...
[M::mem_process_seqs] Processed 2804 reads in 42.853 CPU sec, 42.760 real sec
[M::process] read 2616 sequences (10003265 bp)...
[M::mem_process_seqs] Processed 2722 reads in 43.283 CPU sec, 43.216 real sec
[M::process] read 2762 sequences (10002619 bp)...
[M::mem_process_seqs] Processed 2616 reads in 45.255 CPU sec, 45.166 real sec
[M::process] read 2804 sequences (10001810 bp)...
[M::mem_process_seqs] Processed 2762 reads in 45.119 CPU sec, 45.033 real sec
[M::process] read 2754 sequences (10003868 bp)...
[M::mem_process_seqs] Processed 2804 reads in 45.880 CPU sec, 45.796 real sec
[M::process] read 2736 sequences (10001045 bp)...
[M::mem_process_seqs] Processed 2754 reads in 43.162 CPU sec, 43.071 real sec
[M::process] read 2844 sequences (10001820 bp)...
[M::mem_process_seqs] Processed 2736 reads in 43.266 CPU sec, 43.174 real sec
[M::process] read 2416 sequences (10012848 bp)...
[M::mem_process_seqs] Processed 2844 reads in 42.420 CPU sec, 42.331 real sec
[M::process] read 2656 sequences (10016899 bp)...
[M::mem_process_seqs] Processed 2416 reads in 48.450 CPU sec, 48.356 real sec
[M::process] read 2552 sequences (10001237 bp)...
[M::mem_process_seqs] Processed 2656 reads in 44.571 CPU sec, 44.494 real sec
[M::process] read 2522 sequences (10026662 bp)...
[M::mem_process_seqs] Processed 2552 reads in 44.734 CPU sec, 44.655 real sec
[M::process] read 2716 sequences (10014843 bp)...
[M::mem_process_seqs] Processed 2522 reads in 45.640 CPU sec, 45.550 real sec
[M::process] read 2792 sequences (10008934 bp)...
[M::mem_process_seqs] Processed 2716 reads in 43.429 CPU sec, 43.332 real sec
[M::process] read 2758 sequences (10014984 bp)...
[M::mem_process_seqs] Processed 2792 reads in 43.657 CPU sec, 43.567 real sec
[M::process] read 2742 sequences (10003062 bp)...
[M::mem_process_seqs] Processed 2758 reads in 44.346 CPU sec, 44.253 real sec
[M::process] read 2684 sequences (10000112 bp)...
[M::mem_process_seqs] Processed 2742 reads in 42.943 CPU sec, 42.857 real sec
[M::process] read 2748 sequences (10002126 bp)...
[M::mem_process_seqs] Processed 2684 reads in 43.033 CPU sec, 42.939 real sec
[M::process] read 2704 sequences (10007928 bp)...
[M::mem_process_seqs] Processed 2748 reads in 44.311 CPU sec, 44.218 real sec
[M::process] read 2704 sequences (10010669 bp)...
[M::mem_process_seqs] Processed 2704 reads in 46.441 CPU sec, 46.349 real sec
[M::process] read 2778 sequences (10001164 bp)...
[M::mem_process_seqs] Processed 2704 reads in 46.043 CPU sec, 45.948 real sec
[M::process] read 2772 sequences (10001932 bp)...
[M::mem_process_seqs] Processed 2778 reads in 42.724 CPU sec, 42.631 real sec
[M::process] read 2986 sequences (10004221 bp)...
[M::mem_process_seqs] Processed 2772 reads in 46.294 CPU sec, 46.199 real sec
[M::process] read 3014 sequences (10002450 bp)...
[M::mem_process_seqs] Processed 2986 reads in 42.043 CPU sec, 41.954 real sec
[M::process] read 2726 sequences (10000151 bp)...
[M::mem_process_seqs] Processed 3014 reads in 41.667 CPU sec, 41.571 real sec
[M::process] read 2890 sequences (10009999 bp)...
[M::mem_process_seqs] Processed 2726 reads in 42.731 CPU sec, 42.650 real sec
[M::process] read 2876 sequences (10000590 bp)...
[M::mem_process_seqs] Processed 2890 reads in 42.780 CPU sec, 42.683 real sec
[M::process] read 2736 sequences (10001321 bp)...
[M::mem_process_seqs] Processed 2876 reads in 42.985 CPU sec, 42.921 real sec
[M::process] read 2736 sequences (10005352 bp)...
[M::mem_process_seqs] Processed 2736 reads in 44.592 CPU sec, 44.498 real sec
[M::process] read 2672 sequences (10002731 bp)...
[M::mem_process_seqs] Processed 2736 reads in 46.211 CPU sec, 46.120 real sec
[M::process] read 2806 sequences (10000640 bp)...
[M::mem_process_seqs] Processed 2672 reads in 43.691 CPU sec, 43.591 real sec
[M::process] read 2700 sequences (10012958 bp)...
[M::mem_process_seqs] Processed 2806 reads in 42.409 CPU sec, 42.312 real sec
[M::process] read 2566 sequences (10000368 bp)...
[M::mem_process_seqs] Processed 2700 reads in 43.948 CPU sec, 43.853 real sec
[M::process] read 2626 sequences (10000558 bp)...
[M::mem_process_seqs] Processed 2566 reads in 48.526 CPU sec, 48.442 real sec
[M::process] read 2838 sequences (10000666 bp)...
[M::mem_process_seqs] Processed 2626 reads in 44.474 CPU sec, 44.394 real sec
[M::process] read 2650 sequences (10002196 bp)...
[M::mem_process_seqs] Processed 2838 reads in 42.354 CPU sec, 42.278 real sec
[M::process] read 2804 sequences (10003395 bp)...
[M::mem_process_seqs] Processed 2650 reads in 45.382 CPU sec, 45.285 real sec
[M::process] read 2796 sequences (10010518 bp)...
[M::mem_process_seqs] Processed 2804 reads in 43.538 CPU sec, 43.439 real sec
[M::process] read 2698 sequences (10008794 bp)...
[M::mem_process_seqs] Processed 2796 reads in 43.045 CPU sec, 42.952 real sec
[M::process] read 2568 sequences (10000500 bp)...
[M::mem_process_seqs] Processed 2698 reads in 47.338 CPU sec, 47.256 real sec
[M::process] read 2698 sequences (10006720 bp)...
[M::mem_process_seqs] Processed 2568 reads in 45.805 CPU sec, 45.728 real sec
[M::process] read 2696 sequences (10003570 bp)...
[M::mem_process_seqs] Processed 2698 reads in 42.870 CPU sec, 42.791 real sec
[M::process] read 2724 sequences (10000665 bp)...
[M::mem_process_seqs] Processed 2696 reads in 44.522 CPU sec, 44.424 real sec
[M::process] read 2692 sequences (10015225 bp)...
[M::mem_process_seqs] Processed 2724 reads in 43.911 CPU sec, 43.819 real sec
[M::process] read 2662 sequences (10008764 bp)...
[M::mem_process_seqs] Processed 2692 reads in 47.318 CPU sec, 47.227 real sec
[M::process] read 2614 sequences (10009277 bp)...
[M::mem_process_seqs] Processed 2662 reads in 46.958 CPU sec, 46.875 real sec
[M::process] read 2686 sequences (10001407 bp)...
[M::mem_process_seqs] Processed 2614 reads in 48.068 CPU sec, 47.989 real sec
[M::process] read 2714 sequences (10002775 bp)...
[M::mem_process_seqs] Processed 2686 reads in 45.413 CPU sec, 45.331 real sec
[M::process] read 2740 sequences (10016162 bp)...
[M::mem_process_seqs] Processed 2714 reads in 46.220 CPU sec, 46.141 real sec
[M::process] read 2684 sequences (10003066 bp)...
[M::mem_process_seqs] Processed 2740 reads in 42.014 CPU sec, 41.917 real sec
[M::process] read 2674 sequences (10004792 bp)...
[M::mem_process_seqs] Processed 2684 reads in 44.151 CPU sec, 44.074 real sec
[M::process] read 2732 sequences (10021512 bp)...
[M::mem_process_seqs] Processed 2674 reads in 43.405 CPU sec, 43.314 real sec
[M::process] read 2926 sequences (10000714 bp)...
[M::mem_process_seqs] Processed 2732 reads in 44.300 CPU sec, 44.207 real sec
[M::process] read 2796 sequences (10005935 bp)...
[M::mem_process_seqs] Processed 2926 reads in 41.877 CPU sec, 41.791 real sec
[M::process] read 2728 sequences (10015042 bp)...
[M::mem_process_seqs] Processed 2796 reads in 45.475 CPU sec, 45.380 real sec
[M::process] read 3016 sequences (10000680 bp)...
[M::mem_process_seqs] Processed 2728 reads in 43.510 CPU sec, 43.440 real sec
[M::process] read 2886 sequences (10004765 bp)...
[M::mem_process_seqs] Processed 3016 reads in 41.617 CPU sec, 41.529 real sec
[M::process] read 2628 sequences (10017262 bp)...
[M::mem_process_seqs] Processed 2886 reads in 42.205 CPU sec, 42.119 real sec
[M::process] read 2736 sequences (10007366 bp)...
[M::mem_process_seqs] Processed 2628 reads in 45.979 CPU sec, 45.882 real sec
[M::process] read 2820 sequences (10001724 bp)...
[M::mem_process_seqs] Processed 2736 reads in 44.434 CPU sec, 44.350 real sec
[M::process] read 2760 sequences (10003499 bp)...
[M::mem_process_seqs] Processed 2820 reads in 41.985 CPU sec, 41.922 real sec
[M::process] read 2600 sequences (10005108 bp)...
[M::mem_process_seqs] Processed 2760 reads in 43.761 CPU sec, 43.670 real sec
[M::process] read 2832 sequences (10007934 bp)...
[M::mem_process_seqs] Processed 2600 reads in 44.639 CPU sec, 44.553 real sec
[M::process] read 2826 sequences (10004939 bp)...
[M::mem_process_seqs] Processed 2832 reads in 43.078 CPU sec, 42.987 real sec
[M::process] read 2542 sequences (10005905 bp)...
[M::mem_process_seqs] Processed 2826 reads in 42.498 CPU sec, 42.397 real sec
[M::process] read 2624 sequences (10015209 bp)...
[M::mem_process_seqs] Processed 2542 reads in 45.672 CPU sec, 45.575 real sec
[M::process] read 2776 sequences (10006400 bp)...
[M::mem_process_seqs] Processed 2624 reads in 44.803 CPU sec, 44.741 real sec
[M::process] read 2648 sequences (10015533 bp)...
[M::mem_process_seqs] Processed 2776 reads in 46.001 CPU sec, 45.908 real sec
[M::process] read 2778 sequences (10007561 bp)...
[M::mem_process_seqs] Processed 2648 reads in 45.819 CPU sec, 45.724 real sec
[M::process] read 2984 sequences (10005843 bp)...
[M::mem_process_seqs] Processed 2778 reads in 46.538 CPU sec, 46.445 real sec
[M::process] read 3034 sequences (10010577 bp)...
[M::mem_process_seqs] Processed 2984 reads in 42.102 CPU sec, 42.018 real sec
[M::process] read 2896 sequences (10001745 bp)...
[M::mem_process_seqs] Processed 3034 reads in 42.740 CPU sec, 42.641 real sec
[M::process] read 2728 sequences (10017512 bp)...
[M::mem_process_seqs] Processed 2896 reads in 43.906 CPU sec, 43.827 real sec
[M::process] read 2590 sequences (10007676 bp)...
[M::mem_process_seqs] Processed 2728 reads in 45.701 CPU sec, 45.602 real sec
[M::process] read 2600 sequences (10004430 bp)...
[M::mem_process_seqs] Processed 2590 reads in 46.798 CPU sec, 46.699 real sec
[M::process] read 2726 sequences (10002048 bp)...
[M::mem_process_seqs] Processed 2600 reads in 43.556 CPU sec, 43.495 real sec
[M::process] read 2892 sequences (10004163 bp)...
[M::mem_process_seqs] Processed 2726 reads in 44.501 CPU sec, 44.406 real sec
[M::process] read 2784 sequences (10005676 bp)...
[M::mem_process_seqs] Processed 2892 reads in 41.014 CPU sec, 40.921 real sec
[M::process] read 2648 sequences (10002269 bp)...
[M::mem_process_seqs] Processed 2784 reads in 44.186 CPU sec, 44.090 real sec
[M::process] read 2586 sequences (10000837 bp)...
[M::mem_process_seqs] Processed 2648 reads in 42.725 CPU sec, 42.632 real sec
[M::process] read 2806 sequences (10008465 bp)...
[M::mem_process_seqs] Processed 2586 reads in 44.762 CPU sec, 44.666 real sec
[M::process] read 2796 sequences (10001224 bp)...
[M::mem_process_seqs] Processed 2806 reads in 44.433 CPU sec, 44.349 real sec
[M::process] read 2744 sequences (10000197 bp)...
[M::mem_process_seqs] Processed 2796 reads in 42.135 CPU sec, 42.044 real sec
[M::process] read 2512 sequences (10000232 bp)...
[M::mem_process_seqs] Processed 2744 reads in 45.750 CPU sec, 45.655 real sec
[M::process] read 3014 sequences (10000204 bp)...
[M::mem_process_seqs] Processed 2512 reads in 47.184 CPU sec, 47.119 real sec
[M::process] read 2954 sequences (10000694 bp)...
[M::mem_process_seqs] Processed 3014 reads in 41.470 CPU sec, 41.409 real sec
[M::process] read 2680 sequences (10001527 bp)...
[M::mem_process_seqs] Processed 2954 reads in 42.749 CPU sec, 42.705 real sec
[M::process] read 2740 sequences (10007310 bp)...
[M::mem_process_seqs] Processed 2680 reads in 45.758 CPU sec, 45.687 real sec
[M::process] read 2926 sequences (10001419 bp)...
[M::mem_process_seqs] Processed 2740 reads in 44.209 CPU sec, 44.150 real sec
[M::process] read 2904 sequences (10012514 bp)...
[M::mem_process_seqs] Processed 2926 reads in 43.017 CPU sec, 42.941 real sec
[M::process] read 2878 sequences (10002008 bp)...
[M::mem_process_seqs] Processed 2904 reads in 43.370 CPU sec, 43.307 real sec
[M::process] read 2892 sequences (10013156 bp)...
[M::mem_process_seqs] Processed 2878 reads in 44.532 CPU sec, 44.471 real sec
[M::process] read 2606 sequences (10006231 bp)...
[M::mem_process_seqs] Processed 2892 reads in 42.505 CPU sec, 42.411 real sec
[M::process] read 2710 sequences (10000486 bp)...
[M::mem_process_seqs] Processed 2606 reads in 44.692 CPU sec, 44.626 real sec
[M::process] read 2578 sequences (10000123 bp)...
[M::mem_process_seqs] Processed 2710 reads in 44.306 CPU sec, 44.255 real sec
[M::process] read 2876 sequences (10007492 bp)...
[M::mem_process_seqs] Processed 2578 reads in 43.581 CPU sec, 43.517 real sec
[M::process] read 2946 sequences (10003009 bp)...
[M::mem_process_seqs] Processed 2876 reads in 42.448 CPU sec, 42.392 real sec
[M::process] read 3166 sequences (10006083 bp)...
[M::mem_process_seqs] Processed 2946 reads in 41.637 CPU sec, 41.581 real sec
[M::process] read 3124 sequences (10038621 bp)...
[M::mem_process_seqs] Processed 3166 reads in 41.394 CPU sec, 41.314 real sec
[M::process] read 3106 sequences (10003752 bp)...
[M::mem_process_seqs] Processed 3124 reads in 39.973 CPU sec, 39.896 real sec
[M::process] read 3212 sequences (10005534 bp)...
[M::mem_process_seqs] Processed 3106 reads in 39.308 CPU sec, 39.240 real sec
[M::process] read 2810 sequences (10013183 bp)...
[M::mem_process_seqs] Processed 3212 reads in 40.733 CPU sec, 40.684 real sec
[M::process] read 2708 sequences (10005781 bp)...
[M::mem_process_seqs] Processed 2810 reads in 42.812 CPU sec, 42.759 real sec
[M::process] read 2706 sequences (10001089 bp)...
[M::mem_process_seqs] Processed 2708 reads in 42.609 CPU sec, 42.513 real sec
[M::process] read 2812 sequences (10009506 bp)...
[M::mem_process_seqs] Processed 2706 reads in 43.776 CPU sec, 43.685 real sec
[M::process] read 2794 sequences (10002148 bp)...
[M::mem_process_seqs] Processed 2812 reads in 41.305 CPU sec, 41.216 real sec
[M::process] read 2518 sequences (10017227 bp)...
[M::mem_process_seqs] Processed 2794 reads in 40.706 CPU sec, 40.610 real sec
[M::process] read 2634 sequences (10001825 bp)...
[M::mem_process_seqs] Processed 2518 reads in 44.862 CPU sec, 44.780 real sec
[M::process] read 2654 sequences (10012244 bp)...
[M::mem_process_seqs] Processed 2634 reads in 42.731 CPU sec, 42.634 real sec
[M::process] read 2610 sequences (10004489 bp)...
[M::mem_process_seqs] Processed 2654 reads in 43.354 CPU sec, 43.256 real sec
[M::process] read 2692 sequences (10000300 bp)...
[M::mem_process_seqs] Processed 2610 reads in 46.213 CPU sec, 46.125 real sec
[M::process] read 2682 sequences (10003132 bp)...
[M::mem_process_seqs] Processed 2692 reads in 44.331 CPU sec, 44.242 real sec
[M::process] read 2698 sequences (10010568 bp)...
[M::mem_process_seqs] Processed 2682 reads in 45.486 CPU sec, 45.381 real sec
[M::process] read 2852 sequences (10005177 bp)...
[M::mem_process_seqs] Processed 2698 reads in 45.434 CPU sec, 45.332 real sec
[M::process] read 2904 sequences (10006123 bp)...
[M::mem_process_seqs] Processed 2852 reads in 41.296 CPU sec, 41.203 real sec
[M::process] read 2572 sequences (10001483 bp)...
[M::mem_process_seqs] Processed 2904 reads in 40.273 CPU sec, 40.191 real sec
[M::process] read 2714 sequences (10000554 bp)...
[M::mem_process_seqs] Processed 2572 reads in 43.317 CPU sec, 43.234 real sec
[M::process] read 2744 sequences (10000453 bp)...
[M::mem_process_seqs] Processed 2714 reads in 42.329 CPU sec, 42.239 real sec
[M::process] read 2650 sequences (10000655 bp)...
[M::mem_process_seqs] Processed 2744 reads in 42.204 CPU sec, 42.107 real sec
[M::process] read 2706 sequences (10005217 bp)...
[M::mem_process_seqs] Processed 2650 reads in 45.347 CPU sec, 45.255 real sec
[M::process] read 2628 sequences (10044641 bp)...
[M::mem_process_seqs] Processed 2706 reads in 42.902 CPU sec, 42.809 real sec
[M::process] read 2812 sequences (10007938 bp)...
[M::mem_process_seqs] Processed 2628 reads in 45.291 CPU sec, 45.202 real sec
[M::process] read 3048 sequences (10009991 bp)...
[M::mem_process_seqs] Processed 2812 reads in 45.679 CPU sec, 45.586 real sec
[M::process] read 2902 sequences (10000057 bp)...
[M::mem_process_seqs] Processed 3048 reads in 39.740 CPU sec, 39.647 real sec
[M::process] read 2758 sequences (10006393 bp)...
[M::mem_process_seqs] Processed 2902 reads in 41.115 CPU sec, 41.031 real sec
[M::process] read 2672 sequences (10004995 bp)...
[M::mem_process_seqs] Processed 2758 reads in 43.499 CPU sec, 43.402 real sec
[M::process] read 2626 sequences (10000777 bp)...
[M::mem_process_seqs] Processed 2672 reads in 44.231 CPU sec, 44.140 real sec
[M::process] read 2624 sequences (10003495 bp)...
[M::mem_process_seqs] Processed 2626 reads in 44.250 CPU sec, 44.158 real sec
[M::process] read 2578 sequences (10004942 bp)...
[M::mem_process_seqs] Processed 2624 reads in 44.078 CPU sec, 43.985 real sec
[M::process] read 2738 sequences (10001563 bp)...
[M::mem_process_seqs] Processed 2578 reads in 44.689 CPU sec, 44.596 real sec
[M::process] read 2878 sequences (10011898 bp)...
[M::mem_process_seqs] Processed 2738 reads in 42.380 CPU sec, 42.282 real sec
[M::process] read 2890 sequences (10002038 bp)...
[M::mem_process_seqs] Processed 2878 reads in 42.331 CPU sec, 42.233 real sec
[M::process] read 2766 sequences (10013226 bp)...
[M::mem_process_seqs] Processed 2890 reads in 42.390 CPU sec, 42.293 real sec
[M::process] read 2602 sequences (10026997 bp)...
[M::mem_process_seqs] Processed 2766 reads in 45.070 CPU sec, 44.982 real sec
[M::process] read 2874 sequences (10005126 bp)...
[M::mem_process_seqs] Processed 2602 reads in 46.164 CPU sec, 46.081 real sec
[M::process] read 3096 sequences (10000401 bp)...
[M::mem_process_seqs] Processed 2874 reads in 42.920 CPU sec, 42.832 real sec
[M::process] read 3114 sequences (10010591 bp)...
[M::mem_process_seqs] Processed 3096 reads in 41.955 CPU sec, 41.892 real sec
[M::process] read 2832 sequences (10000667 bp)...
[M::mem_process_seqs] Processed 3114 reads in 42.636 CPU sec, 42.542 real sec
[M::process] read 2888 sequences (10000291 bp)...
[M::mem_process_seqs] Processed 2832 reads in 44.192 CPU sec, 44.101 real sec
[M::process] read 2860 sequences (10006993 bp)...
[M::mem_process_seqs] Processed 2888 reads in 40.834 CPU sec, 40.740 real sec
[M::process] read 2836 sequences (10000426 bp)...
[M::mem_process_seqs] Processed 2860 reads in 42.998 CPU sec, 42.917 real sec
[M::process] read 2626 sequences (10002320 bp)...
[M::mem_process_seqs] Processed 2836 reads in 43.228 CPU sec, 43.129 real sec
[M::process] read 2536 sequences (10004025 bp)...
[M::mem_process_seqs] Processed 2626 reads in 44.844 CPU sec, 44.751 real sec
[M::process] read 2598 sequences (10009810 bp)...
[M::mem_process_seqs] Processed 2536 reads in 44.501 CPU sec, 44.407 real sec
[M::process] read 2514 sequences (10011637 bp)...
[M::mem_process_seqs] Processed 2598 reads in 44.252 CPU sec, 44.164 real sec
[M::process] read 2788 sequences (10006023 bp)...
[M::mem_process_seqs] Processed 2514 reads in 46.695 CPU sec, 46.605 real sec
[M::process] read 2982 sequences (10004450 bp)...
[M::mem_process_seqs] Processed 2788 reads in 45.234 CPU sec, 45.137 real sec
[M::process] read 2950 sequences (10003542 bp)...
[M::mem_process_seqs] Processed 2982 reads in 44.038 CPU sec, 43.951 real sec
[M::process] read 2704 sequences (10006175 bp)...
[M::mem_process_seqs] Processed 2950 reads in 42.887 CPU sec, 42.797 real sec
[M::process] read 2682 sequences (10001756 bp)...
[M::mem_process_seqs] Processed 2704 reads in 43.924 CPU sec, 43.832 real sec
[M::process] read 3224 sequences (10012818 bp)...
[M::mem_process_seqs] Processed 2682 reads in 45.122 CPU sec, 45.026 real sec
[M::process] read 3018 sequences (10013154 bp)...
[M::mem_process_seqs] Processed 3224 reads in 40.377 CPU sec, 40.279 real sec
[M::process] read 2720 sequences (10004305 bp)...
[M::mem_process_seqs] Processed 3018 reads in 43.067 CPU sec, 43.016 real sec
[M::process] read 2720 sequences (10011762 bp)...
[M::mem_process_seqs] Processed 2720 reads in 45.658 CPU sec, 45.564 real sec
[M::process] read 2900 sequences (10005196 bp)...
[M::mem_process_seqs] Processed 2720 reads in 46.538 CPU sec, 46.445 real sec
[M::process] read 2828 sequences (10000158 bp)...
[M::mem_process_seqs] Processed 2900 reads in 41.016 CPU sec, 40.938 real sec
[M::process] read 2706 sequences (10003549 bp)...
[M::mem_process_seqs] Processed 2828 reads in 43.847 CPU sec, 43.755 real sec
[M::process] read 2900 sequences (10023998 bp)...
[M::mem_process_seqs] Processed 2706 reads in 42.386 CPU sec, 42.297 real sec
[M::process] read 2836 sequences (10001311 bp)...
[M::mem_process_seqs] Processed 2900 reads in 42.889 CPU sec, 42.799 real sec
[M::process] read 2666 sequences (10001603 bp)...
[M::mem_process_seqs] Processed 2836 reads in 41.187 CPU sec, 41.092 real sec
[M::process] read 3062 sequences (10001065 bp)...
[M::mem_process_seqs] Processed 2666 reads in 46.225 CPU sec, 46.139 real sec
[M::process] read 3148 sequences (10001350 bp)...
[M::mem_process_seqs] Processed 3062 reads in 42.855 CPU sec, 42.756 real sec
[M::process] read 2814 sequences (10004516 bp)...
[M::mem_process_seqs] Processed 3148 reads in 40.784 CPU sec, 40.689 real sec
[M::process] read 2612 sequences (9437151 bp)...
[M::mem_process_seqs] Processed 2814 reads in 41.124 CPU sec, 41.033 real sec
[M::mem_process_seqs] Processed 2612 reads in 41.139 CPU sec, 41.082 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a -k1 -T7 -A1 -B1 -O1 -E1 -L100 /kb/module/work/tmp/GV048_filtlong_flye.contigs.fa /kb/module/work/tmp/a9fdd887-3447-4f1d-a99c-df1c04aa7bbc.single.fastq
[main] Real time: 14042.660 sec; CPU: 14069.908 sec
command: polypolish polish --fraction_invalid 0.2 --fraction_valid 0.5 --max_errors 10 --min_depth 5 /kb/module/work/tmp/GV048_filtlong_flye.contigs.fa /kb/module/work/tmp/alignments1_c82f3c2a-411d-4680-9a4c-1857e0913429.sam > /kb/module/work/tmp/polypolish_output_4ece6dea-d001-465b-8655-dc7610a9011a.fasta
[1;4;93mStarting Polypolish polish[0m [2m(2025-03-25 20:08:23)[0m
[2m Polypolish is a tool for polishing genome assemblies with short reads.
Unlike other tools in this category, Polypolish uses SAM files where each read
has been aligned to all possible locations (not just a single best location).
This allows it to repair errors in repeat regions that other alignment-based
polishers cannot fix.[0m
Polypolish version: 0.6.0
Input assembly:
/kb/module/work/tmp/GV048_filtlong_flye.contigs.fa
Input short-read alignments:
/kb/module/work/tmp/alignments1_c82f3c2a-411d-4680-9a4c-1857e0913429.sam
Settings:
--fraction_invalid 0.2
--fraction_valid 0.5
--max_errors 10
--min_depth 5
not logging debugging information
[1;4;93mLoading assembly[0m [2m(2025-03-25 20:08:23)[0m
contig_1 (5,711,478 bp)
contig_2 (1,777,000 bp)
[1;4;93mLoading alignments[0m [2m(2025-03-25 20:08:23)[0m
/kb/module/work/tmp/alignments1_c82f3c2a-411d-4680-9a4c-1857e0913429.sam: 1,334,226 alignments from 866,190 reads
Filtering for high-quality end-to-end alignments:
485,067 alignments kept
849,159 alignments discarded
[1;4;93mPolishing assembly sequences[0m [2m(2025-03-25 20:09:04)[0m
[2m For each position in the assembly, Polypolish determines the read depth
at that position and collects all aligned bases. It then polishes the assembly
by looking for positions where the pileup unambiguously supports a different
sequence than the assembly.[0m
Polishing contig_1 (5,711,478 bp):
mean read depth: 112.7x
21 bp have a depth of zero (99.9996% coverage)
0 positions changed (0.0000% of total positions)
estimated pre-polishing sequence accuracy: 100.0000% (Q∞)
Polishing contig_2 (1,777,000 bp):
mean read depth: 113.0x
27 bp have a depth of zero (99.9985% coverage)
0 positions changed (0.0000% of total positions)
estimated pre-polishing sequence accuracy: 100.0000% (Q∞)
[1;4;93mFinished![0m [2m(2025-03-25 20:09:07)[0m
Polished sequence (to stdout):
contig_1_polypolish (5,711,478 bp)
contig_2_polypolish (1,777,000 bp)
Time to run: 0:00:44.644360
Generating and saving report.
Polypolish results saved.