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MAKEFLOW_INPUTS=bwa Correction.py Create_Corrected_AllLRReads.py fastq_reduce ref.fasta sam_cat.sh samtools query.fastq
MAKEFLOW_OUTPUTS=corr.out corr.err Corrected_ref.fasta index.err LowConf.txt ref.fasta.fai mem.err pileup.err sort.err create.err
index.err ref.fasta.sa ref.fasta.pac ref.fasta.bwt ref.fasta.ann ref.fasta.amb : bwa ref.fasta
LOCAL ./bwa index ref.fasta 2> index.err
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query.fastq.751 query.fastq.752 query.fastq.753 query.fastq.754 query.fastq.755 query.fastq.756 query.fastq.757 query.fastq.758 query.fastq.759 query.fastq.760 query.fastq.761 query.fastq.762 query.fastq.763 query.fastq.764 query.fastq.765 query.fastq.766 query.fastq.767 query.fastq.768 query.fastq.769 query.fastq.770 query.fastq.771 query.fastq.772 query.fastq.773 query.fastq.774 query.fastq.775 query.fastq.776 query.fastq.777 query.fastq.778 query.fastq.779 query.fastq.780 query.fastq.781 query.fastq.782 query.fastq.783 query.fastq.784 query.fastq.785 query.fastq.786 query.fastq.787 query.fastq.788 query.fastq.789 query.fastq.790 query.fastq.791 query.fastq.792 query.fastq.793 query.fastq.794 query.fastq.795 query.fastq.796 query.fastq.797 query.fastq.798 query.fastq.799 query.fastq.800 query.fastq.801 query.fastq.802 query.fastq.803 query.fastq.804 query.fastq.805 query.fastq.806 query.fastq.807 query.fastq.808 query.fastq.809 query.fastq.810 query.fastq.811 query.fastq.812 query.fastq.813 query.fastq.814 query.fastq.815 query.fastq.816 query.fastq.817 query.fastq.818 query.fastq.819 query.fastq.820 query.fastq.821 query.fastq.822 query.fastq.823 query.fastq.824 query.fastq.825 query.fastq.826 query.fastq.827 query.fastq.828 query.fastq.829 query.fastq.830 query.fastq.831 query.fastq.832 query.fastq.833 query.fastq.834 query.fastq.835 query.fastq.836 query.fastq.837 query.fastq.838 query.fastq.839 query.fastq.840 query.fastq.841 query.fastq.842 query.fastq.843 query.fastq.844 query.fastq.845 query.fastq.846 query.fastq.847 query.fastq.848 query.fastq.849 query.fastq.850 query.fastq.851 query.fastq.852 query.fastq.853 query.fastq.854 query.fastq.855 query.fastq.856 query.fastq.857 query.fastq.858 query.fastq.859 query.fastq.860 query.fastq.861 query.fastq.862 query.fastq.863 query.fastq.864 query.fastq.865 query.fastq.866 query.fastq.867 query.fastq.868 query.fastq.869 query.fastq.870 query.fastq.871 query.fastq.872 query.fastq.873 query.fastq.874 query.fastq.875 query.fastq.876 query.fastq.877 query.fastq.878 query.fastq.879 query.fastq.880 query.fastq.881 query.fastq.882 query.fastq.883 query.fastq.884 query.fastq.885 query.fastq.886 query.fastq.887 query.fastq.888 query.fastq.889 query.fastq.890 query.fastq.891 query.fastq.892 query.fastq.893 query.fastq.894 query.fastq.895 query.fastq.896 query.fastq.897 query.fastq.898 query.fastq.899 query.fastq.900 query.fastq.901 query.fastq.902 query.fastq.903 query.fastq.904 query.fastq.905 query.fastq.906 query.fastq.907 query.fastq.908 query.fastq.909 query.fastq.910 query.fastq.911 query.fastq.912 query.fastq.913 query.fastq.914 query.fastq.915 query.fastq.916 query.fastq.917 query.fastq.918 query.fastq.919 query.fastq.920 query.fastq.921 query.fastq.922 query.fastq.923 query.fastq.924 query.fastq.925 query.fastq.926 query.fastq.927 query.fastq.928 query.fastq.929 query.fastq.930 query.fastq.931 query.fastq.932 query.fastq.933 query.fastq.934 query.fastq.935 query.fastq.936 query.fastq.937 query.fastq.938 query.fastq.939 query.fastq.940 query.fastq.941 query.fastq.942 query.fastq.943 query.fastq.944 query.fastq.945 query.fastq.946 query.fastq.947 query.fastq.948 query.fastq.949 query.fastq.950 query.fastq.951 query.fastq.952 query.fastq.953 query.fastq.954 query.fastq.955 query.fastq.956 query.fastq.957 query.fastq.958 query.fastq.959 query.fastq.960 query.fastq.961 query.fastq.962 query.fastq.963 query.fastq.964 query.fastq.965 query.fastq.966 query.fastq.967 query.fastq.968 query.fastq.969 query.fastq.970 query.fastq.971 query.fastq.972 query.fastq.973 query.fastq.974 query.fastq.975 query.fastq.976 query.fastq.977 query.fastq.978 query.fastq.979 query.fastq.980 query.fastq.981 query.fastq.982 query.fastq.983 query.fastq.984 query.fastq.985 query.fastq.986 query.fastq.987 query.fastq.988 query.fastq.989 query.fastq.990 query.fastq.991 query.fastq.992 query.fastq.993 query.fastq.994 query.fastq.995 query.fastq.996 query.fastq.997 query.fastq.998 query.fastq.999 : fastq_reduce query.fastq
LOCAL perl fastq_reduce query.fastq 100
Out.0.sam mem.0.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.0
./bwa mem ref.fasta query.fastq.0 > Out.0.sam 2> mem.0.err
Out.1.sam mem.1.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.1
./bwa mem ref.fasta query.fastq.1 > Out.1.sam 2> mem.1.err
Out.2.sam mem.2.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.2
./bwa mem ref.fasta query.fastq.2 > Out.2.sam 2> mem.2.err
Out.3.sam mem.3.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.3
./bwa mem ref.fasta query.fastq.3 > Out.3.sam 2> mem.3.err
Out.4.sam mem.4.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.4
./bwa mem ref.fasta query.fastq.4 > Out.4.sam 2> mem.4.err
Out.5.sam mem.5.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.5
./bwa mem ref.fasta query.fastq.5 > Out.5.sam 2> mem.5.err
Out.6.sam mem.6.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.6
./bwa mem ref.fasta query.fastq.6 > Out.6.sam 2> mem.6.err
Out.7.sam mem.7.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.7
./bwa mem ref.fasta query.fastq.7 > Out.7.sam 2> mem.7.err
Out.8.sam mem.8.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.8
./bwa mem ref.fasta query.fastq.8 > Out.8.sam 2> mem.8.err
Out.9.sam mem.9.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.9
./bwa mem ref.fasta query.fastq.9 > Out.9.sam 2> mem.9.err
Out.10.sam mem.10.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.10
./bwa mem ref.fasta query.fastq.10 > Out.10.sam 2> mem.10.err
Out.11.sam mem.11.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.11
./bwa mem ref.fasta query.fastq.11 > Out.11.sam 2> mem.11.err
Out.12.sam mem.12.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.12
./bwa mem ref.fasta query.fastq.12 > Out.12.sam 2> mem.12.err
Out.13.sam mem.13.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.13
./bwa mem ref.fasta query.fastq.13 > Out.13.sam 2> mem.13.err
Out.14.sam mem.14.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.14
./bwa mem ref.fasta query.fastq.14 > Out.14.sam 2> mem.14.err
Out.15.sam mem.15.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.15
./bwa mem ref.fasta query.fastq.15 > Out.15.sam 2> mem.15.err
Out.16.sam mem.16.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.16
./bwa mem ref.fasta query.fastq.16 > Out.16.sam 2> mem.16.err
Out.17.sam mem.17.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.17
./bwa mem ref.fasta query.fastq.17 > Out.17.sam 2> mem.17.err
Out.18.sam mem.18.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.18
./bwa mem ref.fasta query.fastq.18 > Out.18.sam 2> mem.18.err
Out.19.sam mem.19.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.19
./bwa mem ref.fasta query.fastq.19 > Out.19.sam 2> mem.19.err
Out.20.sam mem.20.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.20
./bwa mem ref.fasta query.fastq.20 > Out.20.sam 2> mem.20.err
Out.21.sam mem.21.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.21
./bwa mem ref.fasta query.fastq.21 > Out.21.sam 2> mem.21.err
Out.22.sam mem.22.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.22
./bwa mem ref.fasta query.fastq.22 > Out.22.sam 2> mem.22.err
Out.23.sam mem.23.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.23
./bwa mem ref.fasta query.fastq.23 > Out.23.sam 2> mem.23.err
Out.24.sam mem.24.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.24
./bwa mem ref.fasta query.fastq.24 > Out.24.sam 2> mem.24.err
Out.25.sam mem.25.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.25
./bwa mem ref.fasta query.fastq.25 > Out.25.sam 2> mem.25.err
Out.26.sam mem.26.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.26
./bwa mem ref.fasta query.fastq.26 > Out.26.sam 2> mem.26.err
Out.27.sam mem.27.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.27
./bwa mem ref.fasta query.fastq.27 > Out.27.sam 2> mem.27.err
Out.28.sam mem.28.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.28
./bwa mem ref.fasta query.fastq.28 > Out.28.sam 2> mem.28.err
Out.29.sam mem.29.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.29
./bwa mem ref.fasta query.fastq.29 > Out.29.sam 2> mem.29.err
Out.30.sam mem.30.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.30
./bwa mem ref.fasta query.fastq.30 > Out.30.sam 2> mem.30.err
Out.31.sam mem.31.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.31
./bwa mem ref.fasta query.fastq.31 > Out.31.sam 2> mem.31.err
Out.32.sam mem.32.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.32
./bwa mem ref.fasta query.fastq.32 > Out.32.sam 2> mem.32.err
Out.33.sam mem.33.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.33
./bwa mem ref.fasta query.fastq.33 > Out.33.sam 2> mem.33.err
Out.34.sam mem.34.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.34
./bwa mem ref.fasta query.fastq.34 > Out.34.sam 2> mem.34.err
Out.35.sam mem.35.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.35
./bwa mem ref.fasta query.fastq.35 > Out.35.sam 2> mem.35.err
Out.36.sam mem.36.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.36
./bwa mem ref.fasta query.fastq.36 > Out.36.sam 2> mem.36.err
Out.37.sam mem.37.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.37
./bwa mem ref.fasta query.fastq.37 > Out.37.sam 2> mem.37.err
Out.38.sam mem.38.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.38
./bwa mem ref.fasta query.fastq.38 > Out.38.sam 2> mem.38.err
Out.39.sam mem.39.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.39
./bwa mem ref.fasta query.fastq.39 > Out.39.sam 2> mem.39.err
Out.40.sam mem.40.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.40
./bwa mem ref.fasta query.fastq.40 > Out.40.sam 2> mem.40.err
Out.41.sam mem.41.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.41
./bwa mem ref.fasta query.fastq.41 > Out.41.sam 2> mem.41.err
Out.42.sam mem.42.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.42
./bwa mem ref.fasta query.fastq.42 > Out.42.sam 2> mem.42.err
Out.43.sam mem.43.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.43
./bwa mem ref.fasta query.fastq.43 > Out.43.sam 2> mem.43.err
Out.44.sam mem.44.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.44
./bwa mem ref.fasta query.fastq.44 > Out.44.sam 2> mem.44.err
Out.45.sam mem.45.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.45
./bwa mem ref.fasta query.fastq.45 > Out.45.sam 2> mem.45.err
Out.46.sam mem.46.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.46
./bwa mem ref.fasta query.fastq.46 > Out.46.sam 2> mem.46.err
Out.47.sam mem.47.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.47
./bwa mem ref.fasta query.fastq.47 > Out.47.sam 2> mem.47.err
Out.48.sam mem.48.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.48
./bwa mem ref.fasta query.fastq.48 > Out.48.sam 2> mem.48.err
Out.49.sam mem.49.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.49
./bwa mem ref.fasta query.fastq.49 > Out.49.sam 2> mem.49.err
Out.50.sam mem.50.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.50
./bwa mem ref.fasta query.fastq.50 > Out.50.sam 2> mem.50.err
Out.51.sam mem.51.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.51
./bwa mem ref.fasta query.fastq.51 > Out.51.sam 2> mem.51.err
Out.52.sam mem.52.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.52
./bwa mem ref.fasta query.fastq.52 > Out.52.sam 2> mem.52.err
Out.53.sam mem.53.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.53
./bwa mem ref.fasta query.fastq.53 > Out.53.sam 2> mem.53.err
Out.54.sam mem.54.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.54
./bwa mem ref.fasta query.fastq.54 > Out.54.sam 2> mem.54.err
Out.55.sam mem.55.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.55
./bwa mem ref.fasta query.fastq.55 > Out.55.sam 2> mem.55.err
Out.56.sam mem.56.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.56
./bwa mem ref.fasta query.fastq.56 > Out.56.sam 2> mem.56.err
Out.57.sam mem.57.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.57
./bwa mem ref.fasta query.fastq.57 > Out.57.sam 2> mem.57.err
Out.58.sam mem.58.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.58
./bwa mem ref.fasta query.fastq.58 > Out.58.sam 2> mem.58.err
Out.59.sam mem.59.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.59
./bwa mem ref.fasta query.fastq.59 > Out.59.sam 2> mem.59.err
Out.60.sam mem.60.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.60
./bwa mem ref.fasta query.fastq.60 > Out.60.sam 2> mem.60.err
Out.61.sam mem.61.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.61
./bwa mem ref.fasta query.fastq.61 > Out.61.sam 2> mem.61.err
Out.62.sam mem.62.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.62
./bwa mem ref.fasta query.fastq.62 > Out.62.sam 2> mem.62.err
Out.63.sam mem.63.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.63
./bwa mem ref.fasta query.fastq.63 > Out.63.sam 2> mem.63.err
Out.64.sam mem.64.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.64
./bwa mem ref.fasta query.fastq.64 > Out.64.sam 2> mem.64.err
Out.65.sam mem.65.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.65
./bwa mem ref.fasta query.fastq.65 > Out.65.sam 2> mem.65.err
Out.66.sam mem.66.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.66
./bwa mem ref.fasta query.fastq.66 > Out.66.sam 2> mem.66.err
Out.67.sam mem.67.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.67
./bwa mem ref.fasta query.fastq.67 > Out.67.sam 2> mem.67.err
Out.68.sam mem.68.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.68
./bwa mem ref.fasta query.fastq.68 > Out.68.sam 2> mem.68.err
Out.69.sam mem.69.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.69
./bwa mem ref.fasta query.fastq.69 > Out.69.sam 2> mem.69.err
Out.70.sam mem.70.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.70
./bwa mem ref.fasta query.fastq.70 > Out.70.sam 2> mem.70.err
Out.71.sam mem.71.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.71
./bwa mem ref.fasta query.fastq.71 > Out.71.sam 2> mem.71.err
Out.72.sam mem.72.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.72
./bwa mem ref.fasta query.fastq.72 > Out.72.sam 2> mem.72.err
Out.73.sam mem.73.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.73
./bwa mem ref.fasta query.fastq.73 > Out.73.sam 2> mem.73.err
Out.74.sam mem.74.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.74
./bwa mem ref.fasta query.fastq.74 > Out.74.sam 2> mem.74.err
Out.75.sam mem.75.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.75
./bwa mem ref.fasta query.fastq.75 > Out.75.sam 2> mem.75.err
Out.76.sam mem.76.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.76
./bwa mem ref.fasta query.fastq.76 > Out.76.sam 2> mem.76.err
Out.77.sam mem.77.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.77
./bwa mem ref.fasta query.fastq.77 > Out.77.sam 2> mem.77.err
Out.78.sam mem.78.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.78
./bwa mem ref.fasta query.fastq.78 > Out.78.sam 2> mem.78.err
Out.79.sam mem.79.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.79
./bwa mem ref.fasta query.fastq.79 > Out.79.sam 2> mem.79.err
Out.80.sam mem.80.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.80
./bwa mem ref.fasta query.fastq.80 > Out.80.sam 2> mem.80.err
Out.81.sam mem.81.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.81
./bwa mem ref.fasta query.fastq.81 > Out.81.sam 2> mem.81.err
Out.82.sam mem.82.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.82
./bwa mem ref.fasta query.fastq.82 > Out.82.sam 2> mem.82.err
Out.83.sam mem.83.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.83
./bwa mem ref.fasta query.fastq.83 > Out.83.sam 2> mem.83.err
Out.84.sam mem.84.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.84
./bwa mem ref.fasta query.fastq.84 > Out.84.sam 2> mem.84.err
Out.85.sam mem.85.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.85
./bwa mem ref.fasta query.fastq.85 > Out.85.sam 2> mem.85.err
Out.86.sam mem.86.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.86
./bwa mem ref.fasta query.fastq.86 > Out.86.sam 2> mem.86.err
Out.87.sam mem.87.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.87
./bwa mem ref.fasta query.fastq.87 > Out.87.sam 2> mem.87.err
Out.88.sam mem.88.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.88
./bwa mem ref.fasta query.fastq.88 > Out.88.sam 2> mem.88.err
Out.89.sam mem.89.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.89
./bwa mem ref.fasta query.fastq.89 > Out.89.sam 2> mem.89.err
Out.90.sam mem.90.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.90
./bwa mem ref.fasta query.fastq.90 > Out.90.sam 2> mem.90.err
Out.91.sam mem.91.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.91
./bwa mem ref.fasta query.fastq.91 > Out.91.sam 2> mem.91.err
Out.92.sam mem.92.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.92
./bwa mem ref.fasta query.fastq.92 > Out.92.sam 2> mem.92.err
Out.93.sam mem.93.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.93
./bwa mem ref.fasta query.fastq.93 > Out.93.sam 2> mem.93.err
Out.94.sam mem.94.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.94
./bwa mem ref.fasta query.fastq.94 > Out.94.sam 2> mem.94.err
Out.95.sam mem.95.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.95
./bwa mem ref.fasta query.fastq.95 > Out.95.sam 2> mem.95.err
Out.96.sam mem.96.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.96
./bwa mem ref.fasta query.fastq.96 > Out.96.sam 2> mem.96.err
Out.97.sam mem.97.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.97
./bwa mem ref.fasta query.fastq.97 > Out.97.sam 2> mem.97.err
Out.98.sam mem.98.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.98
./bwa mem ref.fasta query.fastq.98 > Out.98.sam 2> mem.98.err
Out.99.sam mem.99.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.99
./bwa mem ref.fasta query.fastq.99 > Out.99.sam 2> mem.99.err
Out.100.sam mem.100.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.100
./bwa mem ref.fasta query.fastq.100 > Out.100.sam 2> mem.100.err
Out.101.sam mem.101.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.101
./bwa mem ref.fasta query.fastq.101 > Out.101.sam 2> mem.101.err
Out.102.sam mem.102.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.102
./bwa mem ref.fasta query.fastq.102 > Out.102.sam 2> mem.102.err
Out.103.sam mem.103.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.103
./bwa mem ref.fasta query.fastq.103 > Out.103.sam 2> mem.103.err
Out.104.sam mem.104.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.104
./bwa mem ref.fasta query.fastq.104 > Out.104.sam 2> mem.104.err
Out.105.sam mem.105.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.105
./bwa mem ref.fasta query.fastq.105 > Out.105.sam 2> mem.105.err
Out.106.sam mem.106.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.106
./bwa mem ref.fasta query.fastq.106 > Out.106.sam 2> mem.106.err
Out.107.sam mem.107.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.107
./bwa mem ref.fasta query.fastq.107 > Out.107.sam 2> mem.107.err
Out.108.sam mem.108.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.108
./bwa mem ref.fasta query.fastq.108 > Out.108.sam 2> mem.108.err
Out.109.sam mem.109.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.109
./bwa mem ref.fasta query.fastq.109 > Out.109.sam 2> mem.109.err
Out.110.sam mem.110.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.110
./bwa mem ref.fasta query.fastq.110 > Out.110.sam 2> mem.110.err
Out.111.sam mem.111.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.111
./bwa mem ref.fasta query.fastq.111 > Out.111.sam 2> mem.111.err
Out.112.sam mem.112.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.112
./bwa mem ref.fasta query.fastq.112 > Out.112.sam 2> mem.112.err
Out.113.sam mem.113.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.113
./bwa mem ref.fasta query.fastq.113 > Out.113.sam 2> mem.113.err
Out.114.sam mem.114.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.114
./bwa mem ref.fasta query.fastq.114 > Out.114.sam 2> mem.114.err
Out.115.sam mem.115.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.115
./bwa mem ref.fasta query.fastq.115 > Out.115.sam 2> mem.115.err
Out.116.sam mem.116.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.116
./bwa mem ref.fasta query.fastq.116 > Out.116.sam 2> mem.116.err
Out.117.sam mem.117.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.117
./bwa mem ref.fasta query.fastq.117 > Out.117.sam 2> mem.117.err
Out.118.sam mem.118.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.118
./bwa mem ref.fasta query.fastq.118 > Out.118.sam 2> mem.118.err
Out.119.sam mem.119.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.119
./bwa mem ref.fasta query.fastq.119 > Out.119.sam 2> mem.119.err
Out.120.sam mem.120.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.120
./bwa mem ref.fasta query.fastq.120 > Out.120.sam 2> mem.120.err
Out.121.sam mem.121.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.121
./bwa mem ref.fasta query.fastq.121 > Out.121.sam 2> mem.121.err
Out.122.sam mem.122.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.122
./bwa mem ref.fasta query.fastq.122 > Out.122.sam 2> mem.122.err
Out.123.sam mem.123.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.123
./bwa mem ref.fasta query.fastq.123 > Out.123.sam 2> mem.123.err
Out.124.sam mem.124.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.124
./bwa mem ref.fasta query.fastq.124 > Out.124.sam 2> mem.124.err
Out.125.sam mem.125.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.125
./bwa mem ref.fasta query.fastq.125 > Out.125.sam 2> mem.125.err
Out.126.sam mem.126.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.126
./bwa mem ref.fasta query.fastq.126 > Out.126.sam 2> mem.126.err
Out.127.sam mem.127.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.127
./bwa mem ref.fasta query.fastq.127 > Out.127.sam 2> mem.127.err
Out.128.sam mem.128.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.128
./bwa mem ref.fasta query.fastq.128 > Out.128.sam 2> mem.128.err
Out.129.sam mem.129.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.129
./bwa mem ref.fasta query.fastq.129 > Out.129.sam 2> mem.129.err
Out.130.sam mem.130.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.130
./bwa mem ref.fasta query.fastq.130 > Out.130.sam 2> mem.130.err
Out.131.sam mem.131.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.131
./bwa mem ref.fasta query.fastq.131 > Out.131.sam 2> mem.131.err
Out.132.sam mem.132.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.132
./bwa mem ref.fasta query.fastq.132 > Out.132.sam 2> mem.132.err
Out.133.sam mem.133.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.133
./bwa mem ref.fasta query.fastq.133 > Out.133.sam 2> mem.133.err
Out.134.sam mem.134.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.134
./bwa mem ref.fasta query.fastq.134 > Out.134.sam 2> mem.134.err
Out.135.sam mem.135.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.135
./bwa mem ref.fasta query.fastq.135 > Out.135.sam 2> mem.135.err
Out.136.sam mem.136.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.136
./bwa mem ref.fasta query.fastq.136 > Out.136.sam 2> mem.136.err
Out.137.sam mem.137.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.137
./bwa mem ref.fasta query.fastq.137 > Out.137.sam 2> mem.137.err
Out.138.sam mem.138.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.138
./bwa mem ref.fasta query.fastq.138 > Out.138.sam 2> mem.138.err
Out.139.sam mem.139.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.139
./bwa mem ref.fasta query.fastq.139 > Out.139.sam 2> mem.139.err
Out.140.sam mem.140.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.140
./bwa mem ref.fasta query.fastq.140 > Out.140.sam 2> mem.140.err
Out.141.sam mem.141.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.141
./bwa mem ref.fasta query.fastq.141 > Out.141.sam 2> mem.141.err
Out.142.sam mem.142.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.142
./bwa mem ref.fasta query.fastq.142 > Out.142.sam 2> mem.142.err
Out.143.sam mem.143.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.143
./bwa mem ref.fasta query.fastq.143 > Out.143.sam 2> mem.143.err
Out.144.sam mem.144.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.144
./bwa mem ref.fasta query.fastq.144 > Out.144.sam 2> mem.144.err
Out.145.sam mem.145.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.145
./bwa mem ref.fasta query.fastq.145 > Out.145.sam 2> mem.145.err
Out.146.sam mem.146.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.146
./bwa mem ref.fasta query.fastq.146 > Out.146.sam 2> mem.146.err
Out.147.sam mem.147.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.147
./bwa mem ref.fasta query.fastq.147 > Out.147.sam 2> mem.147.err
Out.148.sam mem.148.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.148
./bwa mem ref.fasta query.fastq.148 > Out.148.sam 2> mem.148.err
Out.149.sam mem.149.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.149
./bwa mem ref.fasta query.fastq.149 > Out.149.sam 2> mem.149.err
Out.150.sam mem.150.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.150
./bwa mem ref.fasta query.fastq.150 > Out.150.sam 2> mem.150.err
Out.151.sam mem.151.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.151
./bwa mem ref.fasta query.fastq.151 > Out.151.sam 2> mem.151.err
Out.152.sam mem.152.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.152
./bwa mem ref.fasta query.fastq.152 > Out.152.sam 2> mem.152.err
Out.153.sam mem.153.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.153
./bwa mem ref.fasta query.fastq.153 > Out.153.sam 2> mem.153.err
Out.154.sam mem.154.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.154
./bwa mem ref.fasta query.fastq.154 > Out.154.sam 2> mem.154.err
Out.155.sam mem.155.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.155
./bwa mem ref.fasta query.fastq.155 > Out.155.sam 2> mem.155.err
Out.156.sam mem.156.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.156
./bwa mem ref.fasta query.fastq.156 > Out.156.sam 2> mem.156.err
Out.157.sam mem.157.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.157
./bwa mem ref.fasta query.fastq.157 > Out.157.sam 2> mem.157.err
Out.158.sam mem.158.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.158
./bwa mem ref.fasta query.fastq.158 > Out.158.sam 2> mem.158.err
Out.159.sam mem.159.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.159
./bwa mem ref.fasta query.fastq.159 > Out.159.sam 2> mem.159.err
Out.160.sam mem.160.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.160
./bwa mem ref.fasta query.fastq.160 > Out.160.sam 2> mem.160.err
Out.161.sam mem.161.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.161
./bwa mem ref.fasta query.fastq.161 > Out.161.sam 2> mem.161.err
Out.162.sam mem.162.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.162
./bwa mem ref.fasta query.fastq.162 > Out.162.sam 2> mem.162.err
Out.163.sam mem.163.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.163
./bwa mem ref.fasta query.fastq.163 > Out.163.sam 2> mem.163.err
Out.164.sam mem.164.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.164
./bwa mem ref.fasta query.fastq.164 > Out.164.sam 2> mem.164.err
Out.165.sam mem.165.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.165
./bwa mem ref.fasta query.fastq.165 > Out.165.sam 2> mem.165.err
Out.166.sam mem.166.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.166
./bwa mem ref.fasta query.fastq.166 > Out.166.sam 2> mem.166.err
Out.167.sam mem.167.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.167
./bwa mem ref.fasta query.fastq.167 > Out.167.sam 2> mem.167.err
Out.168.sam mem.168.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.168
./bwa mem ref.fasta query.fastq.168 > Out.168.sam 2> mem.168.err
Out.169.sam mem.169.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.169
./bwa mem ref.fasta query.fastq.169 > Out.169.sam 2> mem.169.err
Out.170.sam mem.170.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.170
./bwa mem ref.fasta query.fastq.170 > Out.170.sam 2> mem.170.err
Out.171.sam mem.171.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.171
./bwa mem ref.fasta query.fastq.171 > Out.171.sam 2> mem.171.err
Out.172.sam mem.172.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.172
./bwa mem ref.fasta query.fastq.172 > Out.172.sam 2> mem.172.err
Out.173.sam mem.173.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.173
./bwa mem ref.fasta query.fastq.173 > Out.173.sam 2> mem.173.err
Out.174.sam mem.174.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.174
./bwa mem ref.fasta query.fastq.174 > Out.174.sam 2> mem.174.err
Out.175.sam mem.175.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.175
./bwa mem ref.fasta query.fastq.175 > Out.175.sam 2> mem.175.err
Out.176.sam mem.176.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.176
./bwa mem ref.fasta query.fastq.176 > Out.176.sam 2> mem.176.err
Out.177.sam mem.177.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.177
./bwa mem ref.fasta query.fastq.177 > Out.177.sam 2> mem.177.err
Out.178.sam mem.178.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.178
./bwa mem ref.fasta query.fastq.178 > Out.178.sam 2> mem.178.err
Out.179.sam mem.179.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.179
./bwa mem ref.fasta query.fastq.179 > Out.179.sam 2> mem.179.err
Out.180.sam mem.180.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.180
./bwa mem ref.fasta query.fastq.180 > Out.180.sam 2> mem.180.err
Out.181.sam mem.181.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.181
./bwa mem ref.fasta query.fastq.181 > Out.181.sam 2> mem.181.err
Out.182.sam mem.182.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.182
./bwa mem ref.fasta query.fastq.182 > Out.182.sam 2> mem.182.err
Out.183.sam mem.183.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.183
./bwa mem ref.fasta query.fastq.183 > Out.183.sam 2> mem.183.err
Out.184.sam mem.184.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.184
./bwa mem ref.fasta query.fastq.184 > Out.184.sam 2> mem.184.err
Out.185.sam mem.185.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.185
./bwa mem ref.fasta query.fastq.185 > Out.185.sam 2> mem.185.err
Out.186.sam mem.186.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.186
./bwa mem ref.fasta query.fastq.186 > Out.186.sam 2> mem.186.err
Out.187.sam mem.187.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.187
./bwa mem ref.fasta query.fastq.187 > Out.187.sam 2> mem.187.err
Out.188.sam mem.188.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.188
./bwa mem ref.fasta query.fastq.188 > Out.188.sam 2> mem.188.err
Out.189.sam mem.189.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.189
./bwa mem ref.fasta query.fastq.189 > Out.189.sam 2> mem.189.err
Out.190.sam mem.190.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.190
./bwa mem ref.fasta query.fastq.190 > Out.190.sam 2> mem.190.err
Out.191.sam mem.191.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.191
./bwa mem ref.fasta query.fastq.191 > Out.191.sam 2> mem.191.err
Out.192.sam mem.192.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.192
./bwa mem ref.fasta query.fastq.192 > Out.192.sam 2> mem.192.err
Out.193.sam mem.193.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.193
./bwa mem ref.fasta query.fastq.193 > Out.193.sam 2> mem.193.err
Out.194.sam mem.194.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.194
./bwa mem ref.fasta query.fastq.194 > Out.194.sam 2> mem.194.err
Out.195.sam mem.195.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.195
./bwa mem ref.fasta query.fastq.195 > Out.195.sam 2> mem.195.err
Out.196.sam mem.196.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.196
./bwa mem ref.fasta query.fastq.196 > Out.196.sam 2> mem.196.err
Out.197.sam mem.197.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.197
./bwa mem ref.fasta query.fastq.197 > Out.197.sam 2> mem.197.err
Out.198.sam mem.198.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.198
./bwa mem ref.fasta query.fastq.198 > Out.198.sam 2> mem.198.err
Out.199.sam mem.199.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.199
./bwa mem ref.fasta query.fastq.199 > Out.199.sam 2> mem.199.err
Out.200.sam mem.200.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.200
./bwa mem ref.fasta query.fastq.200 > Out.200.sam 2> mem.200.err
Out.201.sam mem.201.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.201
./bwa mem ref.fasta query.fastq.201 > Out.201.sam 2> mem.201.err
Out.202.sam mem.202.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.202
./bwa mem ref.fasta query.fastq.202 > Out.202.sam 2> mem.202.err
Out.203.sam mem.203.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.203
./bwa mem ref.fasta query.fastq.203 > Out.203.sam 2> mem.203.err
Out.204.sam mem.204.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.204
./bwa mem ref.fasta query.fastq.204 > Out.204.sam 2> mem.204.err
Out.205.sam mem.205.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.205
./bwa mem ref.fasta query.fastq.205 > Out.205.sam 2> mem.205.err
Out.206.sam mem.206.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.206
./bwa mem ref.fasta query.fastq.206 > Out.206.sam 2> mem.206.err
Out.207.sam mem.207.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.207
./bwa mem ref.fasta query.fastq.207 > Out.207.sam 2> mem.207.err
Out.208.sam mem.208.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.208
./bwa mem ref.fasta query.fastq.208 > Out.208.sam 2> mem.208.err
Out.209.sam mem.209.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.209
./bwa mem ref.fasta query.fastq.209 > Out.209.sam 2> mem.209.err
Out.210.sam mem.210.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.210
./bwa mem ref.fasta query.fastq.210 > Out.210.sam 2> mem.210.err
Out.211.sam mem.211.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.211
./bwa mem ref.fasta query.fastq.211 > Out.211.sam 2> mem.211.err
Out.212.sam mem.212.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.212
./bwa mem ref.fasta query.fastq.212 > Out.212.sam 2> mem.212.err
Out.213.sam mem.213.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.213
./bwa mem ref.fasta query.fastq.213 > Out.213.sam 2> mem.213.err
Out.214.sam mem.214.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.214
./bwa mem ref.fasta query.fastq.214 > Out.214.sam 2> mem.214.err
Out.215.sam mem.215.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.215
./bwa mem ref.fasta query.fastq.215 > Out.215.sam 2> mem.215.err
Out.216.sam mem.216.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.216
./bwa mem ref.fasta query.fastq.216 > Out.216.sam 2> mem.216.err
Out.217.sam mem.217.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.217
./bwa mem ref.fasta query.fastq.217 > Out.217.sam 2> mem.217.err
Out.218.sam mem.218.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.218
./bwa mem ref.fasta query.fastq.218 > Out.218.sam 2> mem.218.err
Out.219.sam mem.219.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.219
./bwa mem ref.fasta query.fastq.219 > Out.219.sam 2> mem.219.err
Out.220.sam mem.220.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.220
./bwa mem ref.fasta query.fastq.220 > Out.220.sam 2> mem.220.err
Out.221.sam mem.221.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.221
./bwa mem ref.fasta query.fastq.221 > Out.221.sam 2> mem.221.err
Out.222.sam mem.222.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.222
./bwa mem ref.fasta query.fastq.222 > Out.222.sam 2> mem.222.err
Out.223.sam mem.223.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.223
./bwa mem ref.fasta query.fastq.223 > Out.223.sam 2> mem.223.err
Out.224.sam mem.224.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.224
./bwa mem ref.fasta query.fastq.224 > Out.224.sam 2> mem.224.err
Out.225.sam mem.225.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.225
./bwa mem ref.fasta query.fastq.225 > Out.225.sam 2> mem.225.err
Out.226.sam mem.226.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.226
./bwa mem ref.fasta query.fastq.226 > Out.226.sam 2> mem.226.err
Out.227.sam mem.227.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.227
./bwa mem ref.fasta query.fastq.227 > Out.227.sam 2> mem.227.err
Out.228.sam mem.228.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.228
./bwa mem ref.fasta query.fastq.228 > Out.228.sam 2> mem.228.err
Out.229.sam mem.229.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.229
./bwa mem ref.fasta query.fastq.229 > Out.229.sam 2> mem.229.err
Out.230.sam mem.230.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.230
./bwa mem ref.fasta query.fastq.230 > Out.230.sam 2> mem.230.err
Out.231.sam mem.231.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.231
./bwa mem ref.fasta query.fastq.231 > Out.231.sam 2> mem.231.err
Out.232.sam mem.232.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.232
./bwa mem ref.fasta query.fastq.232 > Out.232.sam 2> mem.232.err
Out.233.sam mem.233.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.233
./bwa mem ref.fasta query.fastq.233 > Out.233.sam 2> mem.233.err
Out.234.sam mem.234.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.234
./bwa mem ref.fasta query.fastq.234 > Out.234.sam 2> mem.234.err
Out.235.sam mem.235.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.235
./bwa mem ref.fasta query.fastq.235 > Out.235.sam 2> mem.235.err
Out.236.sam mem.236.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.236
./bwa mem ref.fasta query.fastq.236 > Out.236.sam 2> mem.236.err
Out.237.sam mem.237.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.237
./bwa mem ref.fasta query.fastq.237 > Out.237.sam 2> mem.237.err
Out.238.sam mem.238.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.238
./bwa mem ref.fasta query.fastq.238 > Out.238.sam 2> mem.238.err
Out.239.sam mem.239.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.239
./bwa mem ref.fasta query.fastq.239 > Out.239.sam 2> mem.239.err
Out.240.sam mem.240.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.240
./bwa mem ref.fasta query.fastq.240 > Out.240.sam 2> mem.240.err
Out.241.sam mem.241.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.241
./bwa mem ref.fasta query.fastq.241 > Out.241.sam 2> mem.241.err
Out.242.sam mem.242.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.242
./bwa mem ref.fasta query.fastq.242 > Out.242.sam 2> mem.242.err
Out.243.sam mem.243.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.243
./bwa mem ref.fasta query.fastq.243 > Out.243.sam 2> mem.243.err
Out.244.sam mem.244.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.244
./bwa mem ref.fasta query.fastq.244 > Out.244.sam 2> mem.244.err
Out.245.sam mem.245.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.245
./bwa mem ref.fasta query.fastq.245 > Out.245.sam 2> mem.245.err
Out.246.sam mem.246.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.246
./bwa mem ref.fasta query.fastq.246 > Out.246.sam 2> mem.246.err
Out.247.sam mem.247.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.247
./bwa mem ref.fasta query.fastq.247 > Out.247.sam 2> mem.247.err
Out.248.sam mem.248.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.248
./bwa mem ref.fasta query.fastq.248 > Out.248.sam 2> mem.248.err
Out.249.sam mem.249.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.249
./bwa mem ref.fasta query.fastq.249 > Out.249.sam 2> mem.249.err
Out.250.sam mem.250.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.250
./bwa mem ref.fasta query.fastq.250 > Out.250.sam 2> mem.250.err
Out.251.sam mem.251.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.251
./bwa mem ref.fasta query.fastq.251 > Out.251.sam 2> mem.251.err
Out.252.sam mem.252.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.252
./bwa mem ref.fasta query.fastq.252 > Out.252.sam 2> mem.252.err
Out.253.sam mem.253.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.253
./bwa mem ref.fasta query.fastq.253 > Out.253.sam 2> mem.253.err
Out.254.sam mem.254.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.254
./bwa mem ref.fasta query.fastq.254 > Out.254.sam 2> mem.254.err
Out.255.sam mem.255.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.255
./bwa mem ref.fasta query.fastq.255 > Out.255.sam 2> mem.255.err
Out.256.sam mem.256.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.256
./bwa mem ref.fasta query.fastq.256 > Out.256.sam 2> mem.256.err
Out.257.sam mem.257.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.257
./bwa mem ref.fasta query.fastq.257 > Out.257.sam 2> mem.257.err
Out.258.sam mem.258.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.258
./bwa mem ref.fasta query.fastq.258 > Out.258.sam 2> mem.258.err
Out.259.sam mem.259.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.259
./bwa mem ref.fasta query.fastq.259 > Out.259.sam 2> mem.259.err
Out.260.sam mem.260.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.260
./bwa mem ref.fasta query.fastq.260 > Out.260.sam 2> mem.260.err
Out.261.sam mem.261.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.261
./bwa mem ref.fasta query.fastq.261 > Out.261.sam 2> mem.261.err
Out.262.sam mem.262.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.262
./bwa mem ref.fasta query.fastq.262 > Out.262.sam 2> mem.262.err
Out.263.sam mem.263.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.263
./bwa mem ref.fasta query.fastq.263 > Out.263.sam 2> mem.263.err
Out.264.sam mem.264.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.264
./bwa mem ref.fasta query.fastq.264 > Out.264.sam 2> mem.264.err
Out.265.sam mem.265.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.265
./bwa mem ref.fasta query.fastq.265 > Out.265.sam 2> mem.265.err
Out.266.sam mem.266.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.266
./bwa mem ref.fasta query.fastq.266 > Out.266.sam 2> mem.266.err
Out.267.sam mem.267.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.267
./bwa mem ref.fasta query.fastq.267 > Out.267.sam 2> mem.267.err
Out.268.sam mem.268.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.268
./bwa mem ref.fasta query.fastq.268 > Out.268.sam 2> mem.268.err
Out.269.sam mem.269.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.269
./bwa mem ref.fasta query.fastq.269 > Out.269.sam 2> mem.269.err
Out.270.sam mem.270.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.270
./bwa mem ref.fasta query.fastq.270 > Out.270.sam 2> mem.270.err
Out.271.sam mem.271.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.271
./bwa mem ref.fasta query.fastq.271 > Out.271.sam 2> mem.271.err
Out.272.sam mem.272.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.272
./bwa mem ref.fasta query.fastq.272 > Out.272.sam 2> mem.272.err
Out.273.sam mem.273.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.273
./bwa mem ref.fasta query.fastq.273 > Out.273.sam 2> mem.273.err
Out.274.sam mem.274.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.274
./bwa mem ref.fasta query.fastq.274 > Out.274.sam 2> mem.274.err
Out.275.sam mem.275.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.275
./bwa mem ref.fasta query.fastq.275 > Out.275.sam 2> mem.275.err
Out.276.sam mem.276.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.276
./bwa mem ref.fasta query.fastq.276 > Out.276.sam 2> mem.276.err
Out.277.sam mem.277.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.277
./bwa mem ref.fasta query.fastq.277 > Out.277.sam 2> mem.277.err
Out.278.sam mem.278.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.278
./bwa mem ref.fasta query.fastq.278 > Out.278.sam 2> mem.278.err
Out.279.sam mem.279.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.279
./bwa mem ref.fasta query.fastq.279 > Out.279.sam 2> mem.279.err
Out.280.sam mem.280.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.280
./bwa mem ref.fasta query.fastq.280 > Out.280.sam 2> mem.280.err
Out.281.sam mem.281.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.281
./bwa mem ref.fasta query.fastq.281 > Out.281.sam 2> mem.281.err
Out.282.sam mem.282.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.282
./bwa mem ref.fasta query.fastq.282 > Out.282.sam 2> mem.282.err
Out.283.sam mem.283.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.283
./bwa mem ref.fasta query.fastq.283 > Out.283.sam 2> mem.283.err
Out.284.sam mem.284.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.284
./bwa mem ref.fasta query.fastq.284 > Out.284.sam 2> mem.284.err
Out.285.sam mem.285.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.285
./bwa mem ref.fasta query.fastq.285 > Out.285.sam 2> mem.285.err
Out.286.sam mem.286.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.286
./bwa mem ref.fasta query.fastq.286 > Out.286.sam 2> mem.286.err
Out.287.sam mem.287.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.287
./bwa mem ref.fasta query.fastq.287 > Out.287.sam 2> mem.287.err
Out.288.sam mem.288.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.288
./bwa mem ref.fasta query.fastq.288 > Out.288.sam 2> mem.288.err
Out.289.sam mem.289.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.289
./bwa mem ref.fasta query.fastq.289 > Out.289.sam 2> mem.289.err
Out.290.sam mem.290.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.290
./bwa mem ref.fasta query.fastq.290 > Out.290.sam 2> mem.290.err
Out.291.sam mem.291.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.291
./bwa mem ref.fasta query.fastq.291 > Out.291.sam 2> mem.291.err
Out.292.sam mem.292.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.292
./bwa mem ref.fasta query.fastq.292 > Out.292.sam 2> mem.292.err
Out.293.sam mem.293.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.293
./bwa mem ref.fasta query.fastq.293 > Out.293.sam 2> mem.293.err
Out.294.sam mem.294.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.294
./bwa mem ref.fasta query.fastq.294 > Out.294.sam 2> mem.294.err
Out.295.sam mem.295.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.295
./bwa mem ref.fasta query.fastq.295 > Out.295.sam 2> mem.295.err
Out.296.sam mem.296.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.296
./bwa mem ref.fasta query.fastq.296 > Out.296.sam 2> mem.296.err
Out.297.sam mem.297.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.297
./bwa mem ref.fasta query.fastq.297 > Out.297.sam 2> mem.297.err
Out.298.sam mem.298.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.298
./bwa mem ref.fasta query.fastq.298 > Out.298.sam 2> mem.298.err
Out.299.sam mem.299.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.299
./bwa mem ref.fasta query.fastq.299 > Out.299.sam 2> mem.299.err
Out.300.sam mem.300.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.300
./bwa mem ref.fasta query.fastq.300 > Out.300.sam 2> mem.300.err
Out.301.sam mem.301.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.301
./bwa mem ref.fasta query.fastq.301 > Out.301.sam 2> mem.301.err
Out.302.sam mem.302.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.302
./bwa mem ref.fasta query.fastq.302 > Out.302.sam 2> mem.302.err
Out.303.sam mem.303.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.303
./bwa mem ref.fasta query.fastq.303 > Out.303.sam 2> mem.303.err
Out.304.sam mem.304.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.304
./bwa mem ref.fasta query.fastq.304 > Out.304.sam 2> mem.304.err
Out.305.sam mem.305.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.305
./bwa mem ref.fasta query.fastq.305 > Out.305.sam 2> mem.305.err
Out.306.sam mem.306.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.306
./bwa mem ref.fasta query.fastq.306 > Out.306.sam 2> mem.306.err
Out.307.sam mem.307.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.307
./bwa mem ref.fasta query.fastq.307 > Out.307.sam 2> mem.307.err
Out.308.sam mem.308.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.308
./bwa mem ref.fasta query.fastq.308 > Out.308.sam 2> mem.308.err
Out.309.sam mem.309.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.309
./bwa mem ref.fasta query.fastq.309 > Out.309.sam 2> mem.309.err
Out.310.sam mem.310.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.310
./bwa mem ref.fasta query.fastq.310 > Out.310.sam 2> mem.310.err
Out.311.sam mem.311.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.311
./bwa mem ref.fasta query.fastq.311 > Out.311.sam 2> mem.311.err
Out.312.sam mem.312.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.312
./bwa mem ref.fasta query.fastq.312 > Out.312.sam 2> mem.312.err
Out.313.sam mem.313.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.313
./bwa mem ref.fasta query.fastq.313 > Out.313.sam 2> mem.313.err
Out.314.sam mem.314.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.314
./bwa mem ref.fasta query.fastq.314 > Out.314.sam 2> mem.314.err
Out.315.sam mem.315.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.315
./bwa mem ref.fasta query.fastq.315 > Out.315.sam 2> mem.315.err
Out.316.sam mem.316.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.316
./bwa mem ref.fasta query.fastq.316 > Out.316.sam 2> mem.316.err
Out.317.sam mem.317.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.317
./bwa mem ref.fasta query.fastq.317 > Out.317.sam 2> mem.317.err
Out.318.sam mem.318.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.318
./bwa mem ref.fasta query.fastq.318 > Out.318.sam 2> mem.318.err
Out.319.sam mem.319.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.319
./bwa mem ref.fasta query.fastq.319 > Out.319.sam 2> mem.319.err
Out.320.sam mem.320.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.320
./bwa mem ref.fasta query.fastq.320 > Out.320.sam 2> mem.320.err
Out.321.sam mem.321.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.321
./bwa mem ref.fasta query.fastq.321 > Out.321.sam 2> mem.321.err
Out.322.sam mem.322.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.322
./bwa mem ref.fasta query.fastq.322 > Out.322.sam 2> mem.322.err
Out.323.sam mem.323.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.323
./bwa mem ref.fasta query.fastq.323 > Out.323.sam 2> mem.323.err
Out.324.sam mem.324.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.324
./bwa mem ref.fasta query.fastq.324 > Out.324.sam 2> mem.324.err
Out.325.sam mem.325.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.325
./bwa mem ref.fasta query.fastq.325 > Out.325.sam 2> mem.325.err
Out.326.sam mem.326.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.326
./bwa mem ref.fasta query.fastq.326 > Out.326.sam 2> mem.326.err
Out.327.sam mem.327.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.327
./bwa mem ref.fasta query.fastq.327 > Out.327.sam 2> mem.327.err
Out.328.sam mem.328.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.328
./bwa mem ref.fasta query.fastq.328 > Out.328.sam 2> mem.328.err
Out.329.sam mem.329.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.329
./bwa mem ref.fasta query.fastq.329 > Out.329.sam 2> mem.329.err