1#Link a copy of deduplicated Sliva (LSU and SSU trunc combined) with Us changed to Ts. 2ln -s /global/projectb/sandbox/gaag/bbtools/silva/latest/both_deduped_sorted.fa.gz . 3 4#Aggresively remove similar sequences 5dedupe.sh in=both_deduped_sorted.fa.gz out=dd2_e2_s5.fa.gz s=5 e=2 ordered zl=9 fastawrap=4000 6 7#Less-aggressively remove duplicate sequences 8clumpify.sh in=both_deduped_sorted.fa.gz out=clumped_s2.fa.gz zl=9 s=2 dedupe fastawrap=4000 ow passes=2 9 10#Entropy-mask the sequences 11bbduk.sh -Xmx1g in=dd2_e2_s5.fa.gz out=dd2_e2_s5_masked.fa.gz zl=9 entropy=0.6 entropyk=4 entropywindow=24 maskentropy ordered ow qtrim=rl trimq=1 fastawrap=4000 12bbduk.sh -Xmx1g in=clumped_s2.fa.gz out=clumped_s2_masked.fa.gz zl=9 entropy=0.6 entropyk=4 entropywindow=24 maskentropy ordered ow qtrim=rl trimq=1 fastawrap=4000 13 14#Generate synthetic reads 15randomreads.sh -Xmx31g adderrors=f ref=clumped_s2_masked.fa.gz reads=300m out=synth_s2.fa.gz len=100 zl=6 fastawrap=4000 illuminanames 16randomreads.sh -Xmx8g adderrors=f ref=dd2_e2_s5_masked.fa.gz reads=300m out=synth_e2_s5.fa.gz len=100 zl=6 fastawrap=4000 illuminanames 17 18#Remove duplicate reads 19clumpify.sh in=synth_s2.fa.gz out=synth_s2_clumped_s1.fa.gz reorder zl=9 fastawrap=4000 groups=1 dedupe s=1 rcomp 20clumpify.sh in=synth_e2_s5.fa.gz out=synth_e2_s5_clumped_s1.fa.gz reorder zl=9 fastawrap=4000 groups=1 dedupe s=1 rcomp 21 22#Create baseline kmer sets at different depths for different sensitivites (only one depth is needed) 23kcompress.sh -Xmx31g ow zl=9 pigz=16 min=1000 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers1000A.fa.gz 24kcompress.sh -Xmx31g ow zl=9 pigz=16 min=500 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers500A.fa.gz 25kcompress.sh -Xmx31g ow zl=9 pigz=16 min=200 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers200A.fa.gz 26kcompress.sh -Xmx31g ow zl=9 pigz=16 min=100 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers100A.fa.gz 27kcompress.sh -Xmx31g ow zl=9 pigz=16 min=50 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers50A.fa.gz 28kcompress.sh -Xmx31g ow zl=9 pigz=16 min=40 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers40A.fa.gz 29kcompress.sh -Xmx31g ow zl=9 pigz=16 min=30 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers30A.fa.gz 30kcompress.sh -Xmx31g ow zl=9 pigz=16 min=20 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers20A.fa.gz 31kcompress.sh -Xmx31g ow zl=9 pigz=16 min=10 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers10A.fa.gz 32kcompress.sh -Xmx31g ow zl=9 pigz=16 min=8 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers8A.fa.gz 33kcompress.sh -Xmx31g ow zl=9 pigz=16 min=5 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers5A.fa.gz 34kcompress.sh -Xmx31g ow zl=9 pigz=16 min=3 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers3A.fa.gz 35kcompress.sh -Xmx31g ow zl=9 pigz=16 min=2 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers2A.fa.gz 36kcompress.sh -Xmx31g ow zl=9 pigz=16 min=1 in=dd2_e2_s5_masked.fa.gz out=stdout.fa | clumpify.sh -Xmx16g in=stdin.fa k=16 reorder groups=1 fastawrap=4000 ow zl=9 pigz=16 out=riboKmers1A.fa.gz 37 38#Find the missed synthetic reads 39bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers1000A.fa.gz out=read_misses1000A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 40bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers500A.fa.gz out=read_misses500A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 41bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers200A.fa.gz out=read_misses200A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 42bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers100A.fa.gz out=read_misses100A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 43bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers50A.fa.gz out=read_misses50A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 44bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers40A.fa.gz out=read_misses40A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 45bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers30A.fa.gz out=read_misses30A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 46bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers20A.fa.gz out=read_misses20A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 47bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers10A.fa.gz out=read_misses10A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 48bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers8A.fa.gz out=read_misses8A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 49bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers5A.fa.gz out=read_misses5A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 50bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers3A.fa.gz out=read_misses3A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 51bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers2A.fa.gz out=read_misses2A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 52bbduk.sh -Xmx8g in=synth_e2_s5_clumped_s1.fa.gz ref=riboKmers1A.fa.gz out=read_misses1A.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 53 54#Iterate over each depth to add missed kmers (again, only one depth is needed) 55kcompress.sh -Xmx31g ow min=2000 in=read_misses1000A.fa.gz out=riboKmers1000B.fa.gz fastawrap=4000 ow zl=9 pigz=16 56bbduk.sh -Xmx8g in=read_misses1000A.fa.gz ref=riboKmers1000A.fa.gz,riboKmers1000B.fa.gz out=read_misses1000B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 57kcompress.sh -Xmx31g ow min=1000 in=read_misses1000B.fa.gz out=riboKmers1000C.fa.gz fastawrap=4000 ow zl=9 pigz=16 58bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers1000A.fa.gz,riboKmers1000B.fa.gz,riboKmers1000C.fa.gz out=read_misses1000C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 59kcompress.sh -Xmx31g ow min=500 in=read_misses1000C.fa.gz out=riboKmers1000D.fa.gz fastawrap=4000 ow zl=9 pigz=16 60bbduk.sh -Xmx8g in=read_misses1000C.fa.gz ref=riboKmers1000A.fa.gz,riboKmers1000B.fa.gz,riboKmers1000C.fa.gz,riboKmers1000D.fa.gz out=read_misses1000D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 61kcompress.sh -Xmx31g ow min=250 in=read_misses1000D.fa.gz out=riboKmers1000E.fa.gz fastawrap=4000 ow zl=9 pigz=16 62bbduk.sh -Xmx8g in=read_misses1000D.fa.gz ref=riboKmers1000A.fa.gz,riboKmers1000B.fa.gz,riboKmers1000C.fa.gz,riboKmers1000D.fa.gz,riboKmers1000E.fa.gz out=read_misses1000E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 63kcompress.sh -Xmx31g ow in=riboKmers1000A.fa.gz,riboKmers1000B.fa.gz,riboKmers1000C.fa.gz,riboKmers1000D.fa.gz,riboKmers1000E.fa.gz out=riboKmers1000merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 64clumpify.sh k=16 in=riboKmers1000merged.fa.gz out=riboKmers1000clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 65fuse.sh -Xmx1g ow in=riboKmers1000clumped.fa.gz out=riboKmers1000fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 66 67kcompress.sh -Xmx31g ow min=1000 in=read_misses500A.fa.gz out=riboKmers500B.fa.gz fastawrap=4000 ow zl=9 pigz=16 68bbduk.sh -Xmx8g in=read_misses500A.fa.gz ref=riboKmers500A.fa.gz,riboKmers500B.fa.gz out=read_misses500B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 69kcompress.sh -Xmx31g ow min=500 in=read_misses500B.fa.gz out=riboKmers500C.fa.gz fastawrap=4000 ow zl=9 pigz=16 70bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers500A.fa.gz,riboKmers500B.fa.gz,riboKmers500C.fa.gz out=read_misses500C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 71kcompress.sh -Xmx31g ow min=250 in=read_misses500C.fa.gz out=riboKmers500D.fa.gz fastawrap=4000 ow zl=9 pigz=16 72bbduk.sh -Xmx8g in=read_misses500C.fa.gz ref=riboKmers500A.fa.gz,riboKmers500B.fa.gz,riboKmers500C.fa.gz,riboKmers500D.fa.gz out=read_misses500D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 73kcompress.sh -Xmx31g ow min=125 in=read_misses500D.fa.gz out=riboKmers500E.fa.gz fastawrap=4000 ow zl=9 pigz=16 74bbduk.sh -Xmx8g in=read_misses500D.fa.gz ref=riboKmers500A.fa.gz,riboKmers500B.fa.gz,riboKmers500C.fa.gz,riboKmers500D.fa.gz,riboKmers500E.fa.gz out=read_misses500E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 75kcompress.sh -Xmx31g ow in=riboKmers500A.fa.gz,riboKmers500B.fa.gz,riboKmers500C.fa.gz,riboKmers500D.fa.gz,riboKmers500E.fa.gz out=riboKmers500merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 76clumpify.sh k=16 in=riboKmers500merged.fa.gz out=riboKmers500clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 77fuse.sh -Xmx1g ow in=riboKmers500clumped.fa.gz out=riboKmers500fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 78 79kcompress.sh -Xmx31g ow min=500 in=read_misses200A.fa.gz out=riboKmers200B.fa.gz fastawrap=4000 ow zl=9 pigz=16 80bbduk.sh -Xmx8g in=read_misses200A.fa.gz ref=riboKmers200A.fa.gz,riboKmers200B.fa.gz out=read_misses200B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 81kcompress.sh -Xmx31g ow min=250 in=read_misses200B.fa.gz out=riboKmers200C.fa.gz fastawrap=4000 ow zl=9 pigz=16 82bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers200A.fa.gz,riboKmers200B.fa.gz,riboKmers200C.fa.gz out=read_misses200C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 83kcompress.sh -Xmx31g ow min=125 in=read_misses200C.fa.gz out=riboKmers200D.fa.gz fastawrap=4000 ow zl=9 pigz=16 84bbduk.sh -Xmx8g in=read_misses200C.fa.gz ref=riboKmers200A.fa.gz,riboKmers200B.fa.gz,riboKmers200C.fa.gz,riboKmers200D.fa.gz out=read_misses200D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 85kcompress.sh -Xmx31g ow min=60 in=read_misses200D.fa.gz out=riboKmers200E.fa.gz fastawrap=4000 ow zl=9 pigz=16 86bbduk.sh -Xmx8g in=read_misses200D.fa.gz ref=riboKmers200A.fa.gz,riboKmers200B.fa.gz,riboKmers200C.fa.gz,riboKmers200D.fa.gz,riboKmers200E.fa.gz out=read_misses200E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 87kcompress.sh -Xmx31g ow in=riboKmers200A.fa.gz,riboKmers200B.fa.gz,riboKmers200C.fa.gz,riboKmers200D.fa.gz,riboKmers200E.fa.gz out=riboKmers200merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 88clumpify.sh k=16 in=riboKmers200merged.fa.gz out=riboKmers200clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 89fuse.sh -Xmx1g ow in=riboKmers200clumped.fa.gz out=riboKmers200fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 90 91kcompress.sh -Xmx31g ow min=200 in=read_misses100A.fa.gz out=riboKmers100B.fa.gz fastawrap=4000 ow zl=9 pigz=16 92bbduk.sh -Xmx8g in=read_misses100A.fa.gz ref=riboKmers100A.fa.gz,riboKmers100B.fa.gz out=read_misses100B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 93kcompress.sh -Xmx31g ow min=100 in=read_misses100B.fa.gz out=riboKmers100C.fa.gz fastawrap=4000 ow zl=9 pigz=16 94bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers100A.fa.gz,riboKmers100B.fa.gz,riboKmers100C.fa.gz out=read_misses100C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 95kcompress.sh -Xmx31g ow min=50 in=read_misses100C.fa.gz out=riboKmers100D.fa.gz fastawrap=4000 ow zl=9 pigz=16 96bbduk.sh -Xmx8g in=read_misses100C.fa.gz ref=riboKmers100A.fa.gz,riboKmers100B.fa.gz,riboKmers100C.fa.gz,riboKmers100D.fa.gz out=read_misses100D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 97kcompress.sh -Xmx31g ow min=25 in=read_misses100D.fa.gz out=riboKmers100E.fa.gz fastawrap=4000 ow zl=9 pigz=16 98bbduk.sh -Xmx8g in=read_misses100D.fa.gz ref=riboKmers100A.fa.gz,riboKmers100B.fa.gz,riboKmers100C.fa.gz,riboKmers100D.fa.gz,riboKmers100E.fa.gz out=read_misses100E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 99kcompress.sh -Xmx31g ow in=riboKmers100A.fa.gz,riboKmers100B.fa.gz,riboKmers100C.fa.gz,riboKmers100D.fa.gz,riboKmers100E.fa.gz out=riboKmers100merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 100clumpify.sh k=16 in=riboKmers100merged.fa.gz out=riboKmers100clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 101fuse.sh -Xmx1g ow in=riboKmers100clumped.fa.gz out=riboKmers100fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 102 103kcompress.sh -Xmx31g ow min=100 in=read_misses50A.fa.gz out=riboKmers50B.fa.gz fastawrap=4000 ow zl=9 pigz=16 104bbduk.sh -Xmx8g in=read_misses50A.fa.gz ref=riboKmers50A.fa.gz,riboKmers50B.fa.gz out=read_misses50B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 105kcompress.sh -Xmx31g ow min=50 in=read_misses50B.fa.gz out=riboKmers50C.fa.gz fastawrap=4000 ow zl=9 pigz=16 106bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers50A.fa.gz,riboKmers50B.fa.gz,riboKmers50C.fa.gz out=read_misses50C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 107kcompress.sh -Xmx31g ow min=25 in=read_misses50C.fa.gz out=riboKmers50D.fa.gz fastawrap=4000 ow zl=9 pigz=16 108bbduk.sh -Xmx8g in=read_misses50C.fa.gz ref=riboKmers50A.fa.gz,riboKmers50B.fa.gz,riboKmers50C.fa.gz,riboKmers50D.fa.gz out=read_misses50D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 109kcompress.sh -Xmx31g ow min=12 in=read_misses50D.fa.gz out=riboKmers50E.fa.gz fastawrap=4000 ow zl=9 pigz=16 110bbduk.sh -Xmx8g in=read_misses50D.fa.gz ref=riboKmers50A.fa.gz,riboKmers50B.fa.gz,riboKmers50C.fa.gz,riboKmers50D.fa.gz,riboKmers50E.fa.gz out=read_misses50E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 111kcompress.sh -Xmx31g ow in=riboKmers50A.fa.gz,riboKmers50B.fa.gz,riboKmers50C.fa.gz,riboKmers50D.fa.gz,riboKmers50E.fa.gz out=riboKmers50merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 112clumpify.sh k=16 in=riboKmers50merged.fa.gz out=riboKmers50clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 113fuse.sh -Xmx1g ow in=riboKmers50clumped.fa.gz out=riboKmers50fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 114 115kcompress.sh -Xmx31g ow min=80 in=read_misses40A.fa.gz out=riboKmers40B.fa.gz fastawrap=4000 ow zl=9 pigz=16 116bbduk.sh -Xmx8g in=read_misses40A.fa.gz ref=riboKmers40A.fa.gz,riboKmers40B.fa.gz out=read_misses40B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 117kcompress.sh -Xmx31g ow min=40 in=read_misses40B.fa.gz out=riboKmers40C.fa.gz fastawrap=4000 ow zl=9 pigz=16 118bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers40A.fa.gz,riboKmers40B.fa.gz,riboKmers40C.fa.gz out=read_misses40C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 119kcompress.sh -Xmx31g ow min=20 in=read_misses40C.fa.gz out=riboKmers40D.fa.gz fastawrap=4000 ow zl=9 pigz=16 120bbduk.sh -Xmx8g in=read_misses40C.fa.gz ref=riboKmers40A.fa.gz,riboKmers40B.fa.gz,riboKmers40C.fa.gz,riboKmers40D.fa.gz out=read_misses40D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 121kcompress.sh -Xmx31g ow min=10 in=read_misses40D.fa.gz out=riboKmers40E.fa.gz fastawrap=4000 ow zl=9 pigz=16 122bbduk.sh -Xmx8g in=read_misses40D.fa.gz ref=riboKmers40A.fa.gz,riboKmers40B.fa.gz,riboKmers40C.fa.gz,riboKmers40D.fa.gz,riboKmers40E.fa.gz out=read_misses40E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 123kcompress.sh -Xmx31g ow in=riboKmers40A.fa.gz,riboKmers40B.fa.gz,riboKmers40C.fa.gz,riboKmers40D.fa.gz,riboKmers40E.fa.gz out=riboKmers40merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 124clumpify.sh k=16 in=riboKmers40merged.fa.gz out=riboKmers40clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 125fuse.sh -Xmx1g ow in=riboKmers40clumped.fa.gz out=riboKmers40fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 126 127kcompress.sh -Xmx31g ow min=60 in=read_misses30A.fa.gz out=riboKmers30B.fa.gz fastawrap=4000 ow zl=9 pigz=16 128bbduk.sh -Xmx8g in=read_misses30A.fa.gz ref=riboKmers30A.fa.gz,riboKmers30B.fa.gz out=read_misses30B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 129kcompress.sh -Xmx31g ow min=30 in=read_misses30B.fa.gz out=riboKmers30C.fa.gz fastawrap=4000 ow zl=9 pigz=16 130bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers30A.fa.gz,riboKmers30B.fa.gz,riboKmers30C.fa.gz out=read_misses30C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 131kcompress.sh -Xmx31g ow min=15 in=read_misses30C.fa.gz out=riboKmers30D.fa.gz fastawrap=4000 ow zl=9 pigz=16 132bbduk.sh -Xmx8g in=read_misses30C.fa.gz ref=riboKmers30A.fa.gz,riboKmers30B.fa.gz,riboKmers30C.fa.gz,riboKmers30D.fa.gz out=read_misses30D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 133kcompress.sh -Xmx31g ow min=8 in=read_misses30D.fa.gz out=riboKmers30E.fa.gz fastawrap=4000 ow zl=9 pigz=16 134bbduk.sh -Xmx8g in=read_misses30D.fa.gz ref=riboKmers30A.fa.gz,riboKmers30B.fa.gz,riboKmers30C.fa.gz,riboKmers30D.fa.gz,riboKmers30E.fa.gz out=read_misses30E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 135kcompress.sh -Xmx31g ow in=riboKmers30A.fa.gz,riboKmers30B.fa.gz,riboKmers30C.fa.gz,riboKmers30D.fa.gz,riboKmers30E.fa.gz out=riboKmers30merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 136clumpify.sh k=16 in=riboKmers30merged.fa.gz out=riboKmers30clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 137fuse.sh -Xmx1g ow in=riboKmers30clumped.fa.gz out=riboKmers30fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 138 139kcompress.sh -Xmx31g ow min=40 in=read_misses20A.fa.gz out=riboKmers20B.fa.gz fastawrap=4000 ow zl=9 pigz=16 140bbduk.sh -Xmx8g in=read_misses20A.fa.gz ref=riboKmers20A.fa.gz,riboKmers20B.fa.gz out=read_misses20B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 141kcompress.sh -Xmx31g ow min=20 in=read_misses20B.fa.gz out=riboKmers20C.fa.gz fastawrap=4000 ow zl=9 pigz=16 142bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers20A.fa.gz,riboKmers20B.fa.gz,riboKmers20C.fa.gz out=read_misses20C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 143kcompress.sh -Xmx31g ow min=12 in=read_misses20C.fa.gz out=riboKmers20D.fa.gz fastawrap=4000 ow zl=9 pigz=16 144bbduk.sh -Xmx8g in=read_misses20C.fa.gz ref=riboKmers20A.fa.gz,riboKmers20B.fa.gz,riboKmers20C.fa.gz,riboKmers20D.fa.gz out=read_misses20D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 145kcompress.sh -Xmx31g ow min=7 in=read_misses20D.fa.gz out=riboKmers20E.fa.gz fastawrap=4000 ow zl=9 pigz=16 146bbduk.sh -Xmx8g in=read_misses20D.fa.gz ref=riboKmers20A.fa.gz,riboKmers20B.fa.gz,riboKmers20C.fa.gz,riboKmers20D.fa.gz,riboKmers20E.fa.gz out=read_misses20E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 147kcompress.sh -Xmx31g ow in=riboKmers20A.fa.gz,riboKmers20B.fa.gz,riboKmers20C.fa.gz,riboKmers20D.fa.gz,riboKmers20E.fa.gz out=riboKmers20merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 148clumpify.sh k=16 in=riboKmers20merged.fa.gz out=riboKmers20clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 149fuse.sh -Xmx1g ow in=riboKmers20clumped.fa.gz out=riboKmers20fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 150 151kcompress.sh -Xmx31g ow min=20 in=read_misses10A.fa.gz out=riboKmers10B.fa.gz fastawrap=4000 ow zl=9 pigz=16 152bbduk.sh -Xmx8g in=read_misses10A.fa.gz ref=riboKmers10A.fa.gz,riboKmers10B.fa.gz out=read_misses10B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 153kcompress.sh -Xmx31g ow min=12 in=read_misses10B.fa.gz out=riboKmers10C.fa.gz fastawrap=4000 ow zl=9 pigz=16 154bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers10A.fa.gz,riboKmers10B.fa.gz,riboKmers10C.fa.gz out=read_misses10C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 155kcompress.sh -Xmx31g ow min=8 in=read_misses10C.fa.gz out=riboKmers10D.fa.gz fastawrap=4000 ow zl=9 pigz=16 156bbduk.sh -Xmx8g in=read_misses10C.fa.gz ref=riboKmers10A.fa.gz,riboKmers10B.fa.gz,riboKmers10C.fa.gz,riboKmers10D.fa.gz out=read_misses10D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 157kcompress.sh -Xmx31g ow min=5 in=read_misses10D.fa.gz out=riboKmers10E.fa.gz fastawrap=4000 ow zl=9 pigz=16 158bbduk.sh -Xmx8g in=read_misses10D.fa.gz ref=riboKmers10A.fa.gz,riboKmers10B.fa.gz,riboKmers10C.fa.gz,riboKmers10D.fa.gz,riboKmers10E.fa.gz out=read_misses10E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 159kcompress.sh -Xmx31g ow in=riboKmers10A.fa.gz,riboKmers10B.fa.gz,riboKmers10C.fa.gz,riboKmers10D.fa.gz,riboKmers10E.fa.gz out=riboKmers10merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 160clumpify.sh k=16 in=riboKmers10merged.fa.gz out=riboKmers10clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 161fuse.sh -Xmx1g ow in=riboKmers10clumped.fa.gz out=riboKmers10fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 162 163kcompress.sh -Xmx31g ow min=16 in=read_misses8A.fa.gz out=riboKmers8B.fa.gz fastawrap=4000 ow zl=9 pigz=16 164bbduk.sh -Xmx8g in=read_misses8A.fa.gz ref=riboKmers8A.fa.gz,riboKmers8B.fa.gz out=read_misses8B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 165kcompress.sh -Xmx31g ow min=10 in=read_misses8B.fa.gz out=riboKmers8C.fa.gz fastawrap=4000 ow zl=9 pigz=16 166bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers8A.fa.gz,riboKmers8B.fa.gz,riboKmers8C.fa.gz out=read_misses8C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 167kcompress.sh -Xmx31g ow min=7 in=read_misses8C.fa.gz out=riboKmers8D.fa.gz fastawrap=4000 ow zl=9 pigz=16 168bbduk.sh -Xmx8g in=read_misses8C.fa.gz ref=riboKmers8A.fa.gz,riboKmers8B.fa.gz,riboKmers8C.fa.gz,riboKmers8D.fa.gz out=read_misses8D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 169kcompress.sh -Xmx31g ow min=4 in=read_misses8D.fa.gz out=riboKmers8E.fa.gz fastawrap=4000 ow zl=9 pigz=16 170bbduk.sh -Xmx8g in=read_misses8D.fa.gz ref=riboKmers8A.fa.gz,riboKmers8B.fa.gz,riboKmers8C.fa.gz,riboKmers8D.fa.gz,riboKmers8E.fa.gz out=read_misses8E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 171kcompress.sh -Xmx31g ow in=riboKmers8A.fa.gz,riboKmers8B.fa.gz,riboKmers8C.fa.gz,riboKmers8D.fa.gz,riboKmers8E.fa.gz out=riboKmers8merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 172clumpify.sh k=16 in=riboKmers8merged.fa.gz out=riboKmers8clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 173fuse.sh -Xmx1g ow in=riboKmers8clumped.fa.gz out=riboKmers8fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 174 175kcompress.sh -Xmx31g ow min=12 in=read_misses5A.fa.gz out=riboKmers5B.fa.gz fastawrap=4000 ow zl=9 pigz=16 176bbduk.sh -Xmx8g in=read_misses5A.fa.gz ref=riboKmers5A.fa.gz,riboKmers5B.fa.gz out=read_misses5B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 177kcompress.sh -Xmx31g ow min=8 in=read_misses5B.fa.gz out=riboKmers5C.fa.gz fastawrap=4000 ow zl=9 pigz=16 178bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers5A.fa.gz,riboKmers5B.fa.gz,riboKmers5C.fa.gz out=read_misses5C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 179kcompress.sh -Xmx31g ow min=5 in=read_misses5C.fa.gz out=riboKmers5D.fa.gz fastawrap=4000 ow zl=9 pigz=16 180bbduk.sh -Xmx8g in=read_misses5C.fa.gz ref=riboKmers5A.fa.gz,riboKmers5B.fa.gz,riboKmers5C.fa.gz,riboKmers5D.fa.gz out=read_misses5D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 181kcompress.sh -Xmx31g ow min=3 in=read_misses5D.fa.gz out=riboKmers5E.fa.gz fastawrap=4000 ow zl=9 pigz=16 182bbduk.sh -Xmx8g in=read_misses5D.fa.gz ref=riboKmers5A.fa.gz,riboKmers5B.fa.gz,riboKmers5C.fa.gz,riboKmers5D.fa.gz,riboKmers5E.fa.gz out=read_misses5E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 183kcompress.sh -Xmx31g ow in=riboKmers5A.fa.gz,riboKmers5B.fa.gz,riboKmers5C.fa.gz,riboKmers5D.fa.gz,riboKmers5E.fa.gz out=riboKmers5merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 184clumpify.sh k=16 in=riboKmers5merged.fa.gz out=riboKmers5clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 185fuse.sh -Xmx1g ow in=riboKmers5clumped.fa.gz out=riboKmers5fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 186 187kcompress.sh -Xmx31g ow min=10 in=read_misses3A.fa.gz out=riboKmers3B.fa.gz fastawrap=4000 ow zl=9 pigz=16 188bbduk.sh -Xmx8g in=read_misses3A.fa.gz ref=riboKmers3A.fa.gz,riboKmers3B.fa.gz out=read_misses3B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 189kcompress.sh -Xmx31g ow min=7 in=read_misses3B.fa.gz out=riboKmers3C.fa.gz fastawrap=4000 ow zl=9 pigz=16 190bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers3A.fa.gz,riboKmers3B.fa.gz,riboKmers3C.fa.gz out=read_misses3C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 191kcompress.sh -Xmx31g ow min=4 in=read_misses3C.fa.gz out=riboKmers3D.fa.gz fastawrap=4000 ow zl=9 pigz=16 192bbduk.sh -Xmx8g in=read_misses3C.fa.gz ref=riboKmers3A.fa.gz,riboKmers3B.fa.gz,riboKmers3C.fa.gz,riboKmers3D.fa.gz out=read_misses3D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 193kcompress.sh -Xmx31g ow min=3 in=read_misses3D.fa.gz out=riboKmers3E.fa.gz fastawrap=4000 ow zl=9 pigz=16 194bbduk.sh -Xmx8g in=read_misses3D.fa.gz ref=riboKmers3A.fa.gz,riboKmers3B.fa.gz,riboKmers3C.fa.gz,riboKmers3D.fa.gz,riboKmers3E.fa.gz out=read_misses3E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 195kcompress.sh -Xmx31g ow in=riboKmers3A.fa.gz,riboKmers3B.fa.gz,riboKmers3C.fa.gz,riboKmers3D.fa.gz,riboKmers3E.fa.gz out=riboKmers3merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 196clumpify.sh k=16 in=riboKmers3merged.fa.gz out=riboKmers3clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 197fuse.sh -Xmx1g ow in=riboKmers3clumped.fa.gz out=riboKmers3fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 198 199kcompress.sh -Xmx31g ow min=8 in=read_misses2A.fa.gz out=riboKmers2B.fa.gz fastawrap=4000 ow zl=9 pigz=16 200bbduk.sh -Xmx8g in=read_misses2A.fa.gz ref=riboKmers2A.fa.gz,riboKmers2B.fa.gz out=read_misses2B.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 201kcompress.sh -Xmx31g ow min=6 in=read_misses2B.fa.gz out=riboKmers2C.fa.gz fastawrap=4000 ow zl=9 pigz=16 202bbduk.sh -Xmx8g in=synth_s2_clumped_s1.fa.gz ref=riboKmers2A.fa.gz,riboKmers2B.fa.gz,riboKmers2C.fa.gz out=read_misses2C.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 203kcompress.sh -Xmx31g ow min=4 in=read_misses2C.fa.gz out=riboKmers2D.fa.gz fastawrap=4000 ow zl=9 pigz=16 204bbduk.sh -Xmx8g in=read_misses2C.fa.gz ref=riboKmers2A.fa.gz,riboKmers2B.fa.gz,riboKmers2C.fa.gz,riboKmers2D.fa.gz out=read_misses2D.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 205kcompress.sh -Xmx31g ow min=2 in=read_misses2D.fa.gz out=riboKmers2E.fa.gz fastawrap=4000 ow zl=9 pigz=16 206bbduk.sh -Xmx8g in=read_misses2D.fa.gz ref=riboKmers2A.fa.gz,riboKmers2B.fa.gz,riboKmers2C.fa.gz,riboKmers2D.fa.gz,riboKmers2E.fa.gz out=read_misses2E.fa.gz zl=6 k=31 mm=f ordered fastawrap=4000 ow 207kcompress.sh -Xmx31g ow in=riboKmers2A.fa.gz,riboKmers2B.fa.gz,riboKmers2C.fa.gz,riboKmers2D.fa.gz,riboKmers2E.fa.gz out=riboKmers2merged.fa.gz fastawrap=4000 ow zl=9 pigz=16 208clumpify.sh k=16 in=riboKmers2merged.fa.gz out=riboKmers2clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 209fuse.sh -Xmx1g ow in=riboKmers2clumped.fa.gz out=riboKmers2fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 210 211clumpify.sh k=16 in=riboKmers1A.fa.gz out=riboKmers1clumped.fa.gz g=1 zl=9 fastawrap=4000 reorder rcomp ow 212fuse.sh -Xmx1g ow in=riboKmers1A.fa.gz out=riboKmers1fused.fa.gz fastawrap=8000 ow zl=11 pigz=32 maxlen=4000 npad=1 213 214 215