Starting /dee2/code/volunteer_pipeline.sh SRR7472587 current disk space = 3087931613184 free memory = 1495582552 SRR7472587 SRAfilesize 8fef3065188de38be69433d1347f8ecf SRR7472587.sra SRR7472587.sra file validated SRR7472587 is single end SRR7472587 is conventional basespace SRR7472587 read1 length is 51 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7472587_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.089 34.0 33.0 34.0 32.0 34.0 2 33.21575 34.0 33.0 34.0 33.0 34.0 3 33.281 34.0 34.0 34.0 33.0 34.0 4 33.2815 34.0 34.0 34.0 33.0 34.0 5 33.2385 34.0 34.0 34.0 33.0 34.0 6 37.06425 38.0 38.0 38.0 36.0 38.0 7 37.17925 38.0 38.0 38.0 37.0 38.0 8 37.2885 38.0 38.0 38.0 37.0 38.0 9 37.2045 38.0 38.0 38.0 37.0 38.0 10 36.5425 38.0 38.0 38.0 35.0 38.0 11 37.149 38.0 38.0 38.0 37.0 38.0 12 37.2335 38.0 38.0 38.0 37.0 38.0 13 37.188 38.0 38.0 38.0 37.0 38.0 14 37.2055 38.0 38.0 38.0 37.0 38.0 15 37.257 38.0 38.0 38.0 38.0 38.0 16 37.2065 38.0 38.0 38.0 37.0 38.0 17 37.1885 38.0 38.0 38.0 37.0 38.0 18 37.17575 38.0 38.0 38.0 37.0 38.0 19 37.26775 38.0 38.0 38.0 37.0 38.0 20 37.21 38.0 38.0 38.0 37.0 38.0 21 37.153 38.0 38.0 38.0 37.0 38.0 22 37.11375 38.0 38.0 38.0 37.0 38.0 23 37.19325 38.0 38.0 38.0 37.0 38.0 24 37.10575 38.0 38.0 38.0 37.0 38.0 25 37.2525 38.0 38.0 38.0 37.0 38.0 26 37.23675 38.0 38.0 38.0 37.0 38.0 27 37.28925 38.0 38.0 38.0 38.0 38.0 28 37.204 38.0 38.0 38.0 37.0 38.0 29 37.244 38.0 38.0 38.0 38.0 38.0 30 37.2665 38.0 38.0 38.0 38.0 38.0 31 37.12125 38.0 38.0 38.0 37.0 38.0 32 37.141 38.0 38.0 38.0 37.0 38.0 33 37.1815 38.0 38.0 38.0 37.0 38.0 34 37.27775 38.0 38.0 38.0 38.0 38.0 35 37.2475 38.0 38.0 38.0 38.0 38.0 36 36.86775 38.0 38.0 38.0 36.0 38.0 37 37.225 38.0 38.0 38.0 38.0 38.0 38 37.2805 38.0 38.0 38.0 38.0 38.0 39 37.2825 38.0 38.0 38.0 38.0 38.0 40 37.2975 38.0 38.0 38.0 38.0 38.0 41 37.26025 38.0 38.0 38.0 38.0 38.0 42 37.17 38.0 38.0 38.0 38.0 38.0 43 37.23575 38.0 38.0 38.0 38.0 38.0 44 37.26425 38.0 38.0 38.0 38.0 38.0 45 37.298 38.0 38.0 38.0 38.0 38.0 46 37.35875 38.0 38.0 38.0 38.0 38.0 47 37.2015 38.0 38.0 38.0 38.0 38.0 48 37.29525 38.0 38.0 38.0 38.0 38.0 49 37.31425 38.0 38.0 38.0 38.0 38.0 50 37.30125 38.0 38.0 38.0 38.0 38.0 51 37.2185 38.0 38.0 38.0 38.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 17.0 3 0.0 4 1.0 5 4.0 6 2.0 7 2.0 8 0.0 9 0.0 10 1.0 11 0.0 12 0.0 13 1.0 14 1.0 15 0.0 16 1.0 17 2.0 18 1.0 19 0.0 20 1.0 21 3.0 22 1.0 23 1.0 24 3.0 25 1.0 26 5.0 27 11.0 28 6.0 29 12.0 30 12.0 31 26.0 32 43.0 33 55.0 34 70.0 35 90.0 36 292.0 37 3335.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.299999999999997 25.674999999999997 26.35 18.675 2 29.75 19.675 22.3 28.275 3 29.7 22.15 21.55 26.6 4 40.150000000000006 22.0 14.899999999999999 22.95 5 29.625 30.875000000000004 17.75 21.75 6 23.075000000000003 26.474999999999998 24.325 26.125 7 32.425 20.349999999999998 25.35 21.875 8 25.25 26.200000000000003 30.775000000000002 17.775 9 27.03851925962982 32.14107053526764 20.710355177588795 20.110055027513756 10 37.525 25.85 17.25 19.375 11 30.575000000000003 18.875 21.775 28.775000000000002 12 26.575 19.2 29.7 24.525 13 22.5 19.075 27.150000000000002 31.275 14 19.725 36.1 22.875 21.3 15 31.6 32.475 19.475 16.45 16 24.625 27.224999999999998 26.3 21.85 17 25.424999999999997 20.325 35.225 19.025 18 36.625 19.225 23.375 20.775 19 28.925 21.65 29.75 19.675 20 25.674999999999997 29.5 25.124999999999996 19.7 21 26.424999999999997 30.325000000000003 22.85 20.4 22 24.175 25.7 32.5 17.625 23 31.674999999999997 23.575 27.800000000000004 16.950000000000003 24 31.175000000000004 25.324999999999996 25.324999999999996 18.175 25 25.85 28.4 34.849999999999994 10.9 26 30.890445222611305 27.66383191595798 25.662831415707853 15.78289144572286 27 28.9 18.55 32.35 20.200000000000003 28 23.225 25.374999999999996 33.225 18.175 29 26.224999999999998 19.5 26.424999999999997 27.85 30 23.3 12.5 47.125 17.075000000000003 31 30.675 9.65 29.625 30.049999999999997 32 38.27870903177383 8.506379784838629 21.115836877658246 32.099074305729296 33 35.675000000000004 12.8 29.125 22.400000000000002 34 39.65 17.525 19.775000000000002 23.05 35 40.125 15.024999999999999 28.175 16.675 36 50.175000000000004 13.100000000000001 20.225 16.5 37 38.625 18.125 13.375 29.875 38 25.0 24.175 23.45 27.375 39 28.525 32.725 13.0 25.75 40 26.1 31.2 12.775 29.925 41 32.925 24.224999999999998 15.925 26.924999999999997 42 34.2513770655984 29.86980470706059 11.542313470205308 24.336504757135703 43 22.975 38.0 14.000000000000002 25.025 44 33.375 35.575 9.675 21.375 45 31.525 24.224999999999998 10.274999999999999 33.975 46 19.189392044033024 27.395546659994995 23.792844633475106 29.622216662496875 47 16.400000000000002 32.0 14.299999999999999 37.3 48 16.0 27.825 13.225000000000001 42.95 49 18.15 27.500000000000004 18.775 35.575 50 24.8 22.3 11.125 41.775 51 14.025000000000002 32.975 18.825 34.175 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.5 27 1.0 28 0.5 29 0.0 30 0.0 31 0.0 32 0.5 33 1.0 34 2.5 35 4.0 36 5.5 37 7.0 38 12.5 39 18.0 40 33.5 41 49.0 42 83.0 43 117.0 44 139.0 45 161.0 46 224.0 47 287.0 48 312.5 49 338.0 50 497.0 51 656.0 52 648.5 53 641.0 54 581.5 55 522.0 56 602.0 57 682.0 58 458.5 59 235.0 60 181.0 61 127.0 62 109.0 63 91.0 64 62.0 65 33.0 66 22.5 67 12.0 68 11.5 69 11.0 70 6.5 71 2.0 72 3.5 73 5.0 74 2.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.05 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.05 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.075 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.15 43 0.0 44 0.0 45 0.0 46 0.075 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 51 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 57.599999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 88.45486111111111 50.949999999999996 2 4.904513888888888 5.65 3 1.8663194444444444 3.225 4 1.215277777777778 2.8000000000000003 5 0.6944444444444444 2.0 6 0.5208333333333333 1.7999999999999998 7 0.2170138888888889 0.8750000000000001 8 0.1736111111111111 0.8 9 0.2170138888888889 1.125 >10 1.4322916666666665 14.325 >50 0.2170138888888889 9.275 >100 0.08680555555555555 7.175 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 172 4.3 RNA PCR Primer, Index 1 (100% over 30bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 115 2.875 RNA PCR Primer, Index 1 (100% over 22bp) CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 90 2.25 RNA PCR Primer, Index 1 (100% over 28bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 84 2.1 RNA PCR Primer, Index 1 (100% over 30bp) GGGGATGTAGCTCAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 73 1.825 RNA PCR Primer, Index 7 (100% over 35bp) GGGCCTGTAGCTCAGAGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 65 1.625 RNA PCR Primer, Index 1 (100% over 32bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 29bp) TTTGGATTGAAGGGAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 31bp) ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 31bp) ATCCGGTTAGGATCGATCTAAACCAGCCCTGGAATTCTCGGGTGCCAAGGA 30 0.75 RNA PCR Primer, Index 1 (100% over 22bp) GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 30 0.75 No Hit TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 27 0.675 RNA PCR Primer, Index 1 (100% over 26bp) AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 25 0.625 RNA PCR Primer, Index 1 (100% over 30bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 23 0.575 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGCC 22 0.5499999999999999 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC 21 0.525 RNA PCR Primer, Index 7 (100% over 51bp) CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 21 0.525 RNA PCR Primer, Index 1 (100% over 27bp) CATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAAC 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 24bp) TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 29bp) TTTGGATTGAAGGGAGCTCTATGGAATTCTCGGGTGCCAAGGAACTCCAGT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 30bp) GGGGTTGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 15 0.375 RNA PCR Primer, Index 7 (100% over 35bp) GCGCCTGTAGCTCAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 15 0.375 RNA PCR Primer, Index 1 (100% over 32bp) GGGGATGTAGCTCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 14 0.35000000000000003 RNA PCR Primer, Index 7 (100% over 35bp) CAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 32bp) ATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 25bp) TGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 14 0.35000000000000003 RNA PCR Primer, Index 7 (100% over 35bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTGC 13 0.325 No Hit CGCGGGGTAGAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 13 0.325 RNA PCR Primer, Index 2 (100% over 34bp) CCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG 13 0.325 RNA PCR Primer, Index 7 (100% over 36bp) AGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) GCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) TCTTTCCAACGCCTCCCATACCTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) GTGGGAATGAACATTATGAGATGGAATTCTCGGGTGCCAAGGAACTCCAGT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 30bp) ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG 11 0.27499999999999997 RNA PCR Primer, Index 7 (100% over 36bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 33bp) GGGGGTGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 11 0.27499999999999997 RNA PCR Primer, Index 7 (100% over 35bp) CCAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 32bp) GGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGAT 10 0.25 RNA PCR Primer, Index 7 (100% over 38bp) GGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) GACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 9 0.22499999999999998 RNA PCR Primer, Index 2 (100% over 34bp) TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) GTCGGGATAGCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 9 0.22499999999999998 RNA PCR Primer, Index 7 (100% over 35bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGTGGAATTCTCGGGTGCCA 8 0.2 No Hit ACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 8 0.2 RNA PCR Primer, Index 7 (100% over 35bp) GTCGGGATAGCTCAGCAGGTAGAGCAGAGGACTGATGGAATTCTCGGGTGC 8 0.2 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCAA 8 0.2 No Hit CAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 33bp) GGTCGAGGGCACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GATGGAGGACGAGGAAGTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) AAAGGATTGAGCCGAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 6 0.15 RNA PCR Primer, Index 2 (100% over 34bp) TTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GGGGATGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 6 0.15 RNA PCR Primer, Index 7 (100% over 35bp) ATCCGGTTAGGATCGATCTAAACCAGCCTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CCCGGTAGGACCTCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 6 0.15 RNA PCR Primer, Index 7 (100% over 35bp) GAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GCGGATGTAGCCAAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 6 0.15 RNA PCR Primer, Index 1 (100% over 32bp) CAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) TCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CGCGGGGTAGAGCAGCTTGGTAGCTCGCAAGGCTCTGGAATTCTCGGGTGC 6 0.15 No Hit AGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) CATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 5 0.125 RNA PCR Primer, Index 1 (100% over 33bp) CCACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 5 0.125 RNA PCR Primer, Index 2 (100% over 34bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCCA 5 0.125 No Hit TTTTCCCTACTCCACCCATCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GCGGATATAGTCGAATGGTAAAATTTCTCTTTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) ACCCCAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GTCGGGATAGCTCAGCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 5 0.125 RNA PCR Primer, Index 2 (100% over 34bp) TGCGTAGAGATCGGAAAGAACACCAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TCTTGCCTACTCCTCCCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCTGGAATTCTCGGGTGCC 5 0.125 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGGAATTCTCGGGTGCCAA 5 0.125 No Hit AACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) AGTTACTAATTCATGATCTGGCATATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) AGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAATTCTCGGGTGCCA 5 0.125 No Hit AGTTACTAATTCATGATCTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.55 0.0 0.0 0.0 2 0.0 0.55 0.0 0.0 0.0 3 0.0 0.55 0.0 0.0 0.0 4 0.0 0.55 0.0 0.0 0.0 5 0.0 0.55 0.0 0.0 0.0 6 0.0 0.575 0.0 0.0 0.0 7 0.0 0.6 0.0 0.0 0.0 8 0.0 0.65 0.0 0.0 0.0 9 0.0 0.825 0.0 0.0 0.0 10 0.0 0.85 0.0 0.0 0.0 11 0.0 1.025 0.0 0.0 0.0 12 0.0 1.575 0.0 0.0 0.0 13 0.0 1.95 0.0 0.0 0.0 14 0.0 2.85 0.0 0.0 0.0 15 0.0 3.775 0.0 0.0 0.0 16 0.0 5.725 0.0 0.0 0.0 17 0.0 11.575 0.0 0.0 0.0 18 0.0 14.625 0.0 0.0 0.0 19 0.0 17.775 0.0 0.0 0.0 20 0.0 22.725 0.0 0.0 0.0 21 0.0 27.625 0.0 0.0 0.0 22 0.0 41.525 0.0 0.0 0.0 23 0.0 48.8 0.0 0.0 0.0 24 0.0 55.1 0.0 0.0 0.0 25 0.0 66.225 0.0 0.0 0.0 26 0.0 70.375 0.0 0.0 0.0 27 0.0 73.375 0.0 0.0 0.0 28 0.0 75.825 0.0 0.0 0.0 29 0.0 77.8 0.0 0.0 0.0 30 0.0 83.675 0.0 0.0 0.0 31 0.0 85.25 0.0 0.0 0.0 32 0.0 86.8 0.0 0.0 0.0 33 0.0 89.125 0.0 0.0 0.0 34 0.0 92.35 0.0 0.0 0.0 35 0.0 94.475 0.0 0.0 0.0 36 0.0 95.85 0.0 0.0 0.0 37 0.0 96.65 0.0 0.0 0.0 38 0.0 96.8 0.0 0.0 0.0 39 0.0 96.925 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCAAGGC 20 6.222983E-4 45.0 21 AGCTCAA 20 6.222983E-4 45.0 9 GAGGATG 25 3.236105E-5 45.0 15 AGCCAAG 20 6.222983E-4 45.0 10 TTGTAGT 20 6.222983E-4 45.0 5 AGGATGG 25 3.236105E-5 45.0 16 CCTGTAG 25 3.236105E-5 45.0 4 TAGCTCA 50 1.0913936E-11 45.0 8 TAGCCAA 20 6.222983E-4 45.0 9 GGATCAA 20 6.222983E-4 45.0 18 CATTCCC 20 6.222983E-4 45.0 14 CGGATGT 20 6.222983E-4 45.0 3 GCGGATG 20 6.222983E-4 45.0 2 CAGAGGA 25 3.236105E-5 45.0 13 TCAAATG 25 3.236105E-5 45.0 12 TTCCCCT 20 6.222983E-4 45.0 16 GGCCTGT 25 3.236105E-5 45.0 2 TCAGAGG 25 3.236105E-5 45.0 12 CCCTGGA 20 6.222983E-4 45.0 19 CTCAGAG 25 3.236105E-5 45.0 11 >>END_MODULE Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496100 READS because READLEN < 1 Read 496100 spots for SRR7472587.sra Written 496100 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra Rejected 496088 READS because READLEN < 1 Read 496088 spots for SRR7472587.sra Written 496088 spots for SRR7472587.sra SRR ids: ['SRR7472587.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_smt54sy6 SRR7472587.sra spots: 9921772 blocks: [[1, 496088], [496089, 992176], [992177, 1488264], [1488265, 1984352], [1984353, 2480440], [2480441, 2976528], [2976529, 3472616], [3472617, 3968704], [3968705, 4464792], [4464793, 4960880], [4960881, 5456968], [5456969, 5953056], [5953057, 6449144], [6449145, 6945232], [6945233, 7441320], [7441321, 7937408], [7937409, 8433496], [8433497, 8929584], [8929585, 9425672], [9425673, 9921772]] SRR7472587 file size 1393080 SRR7472587 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR7472587 SRR7472587_1.fastq Input file: SRR7472587_1.fastq trimmed: SRR7472587-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Thu Feb 13 18:28:11 2025 >> started Thu Feb 13 18:28:15 2025 >> done (4.107s) 9921772 reads processed; of these: 6673 ( 0.07%) short reads filtered out after trimming by size control 12685 ( 0.13%) empty reads filtered out after trimming by size control 9902414 (99.80%) reads available; of these: 19716 ( 0.20%) trimmed reads available after processing 9882698 (99.80%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 191 0.00% 19 303 0.00% 20 201 0.00% 21 252 0.00% 22 251 0.00% 23 211 0.00% 24 189 0.00% 25 264 0.00% 26 266 0.00% 27 204 0.00% 28 268 0.00% 29 326 0.00% 30 250 0.00% 31 318 0.00% 32 243 0.00% 33 259 0.00% 34 314 0.00% 35 353 0.00% 36 331 0.00% 37 285 0.00% 38 311 0.00% 39 389 0.00% 40 449 0.00% 41 387 0.00% 42 570 0.01% 43 578 0.01% 44 652 0.01% 45 867 0.01% 46 913 0.01% 47 1242 0.01% 48 1406 0.01% 49 1541 0.02% 50 5132 0.05% 51 9882698 99.80% 9902414 reads passed initial QC criterion=sequence-density sequence-density=97.57 sequence-density-rank=1 fanout-score=26.46 fanout-score-rank=1 prefix-density=97.70 prefix-fanout=26.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCG criterion=fanout-score sequence-density=97.57 sequence-density-rank=1 fanout-score=26.46 fanout-score-rank=1 prefix-density=97.70 prefix-fanout=26.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCG Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCG -o SRR7472587 - Input file: STDIN trimmed: SRR7472587-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Thu Feb 13 18:28:35 2025 >> started Thu Feb 13 18:28:41 2025 >> done (6.868s) 9700324 reads processed; of these: 1354967 (13.97%) short reads filtered out after trimming by size control 46993 ( 0.48%) empty reads filtered out after trimming by size control 8298364 (85.55%) reads available; of these: 8196376 (98.77%) trimmed reads available after processing 101988 ( 1.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 282531 3.40% 19 485316 5.85% 20 504731 6.08% 21 1453449 17.51% 22 727278 8.76% 23 623111 7.51% 24 1137294 13.71% 25 412233 4.97% 26 274410 3.31% 27 254979 3.07% 28 222056 2.68% 29 527145 6.35% 30 158746 1.91% 31 150996 1.82% 32 222146 2.68% 33 318626 3.84% 34 161020 1.94% 35 135409 1.63% 36 75955 0.92% 37 27488 0.33% 38 16958 0.20% 39 8700 0.10% 40 6161 0.07% 41 3722 0.04% 42 3765 0.05% 43 1582 0.02% 44 1007 0.01% 45 768 0.01% 46 594 0.01% 47 607 0.01% 48 1388 0.02% 49 355 0.00% 50 616 0.01% 51 97222 1.17% criterion=sequence-density sequence-density=3.61 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=15 prefix-density=0.06 prefix-fanout=1.0 sequence=GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAA criterion=fanout-score sequence-density=0.25 sequence-density-rank=19 fanout-score=11.69 fanout-score-rank=1 prefix-density=2.39 prefix-fanout=1.2 sequence=GAAGGGAGCTCCCTT Started job on | Feb 13 18:28:56 Started mapping on | Feb 13 18:28:57 Finished on | Feb 13 18:29:20 Mapping speed, Million of reads per hour | 1330.51 Number of input reads | 8500454 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 3262810 Uniquely mapped reads % | 38.38% Average mapped length | 24.59 Number of splices: Total | 21762 Number of splices: Annotated (sjdb) | 10507 Number of splices: GT/AG | 20923 Number of splices: GC/AG | 248 Number of splices: AT/AC | 38 Number of splices: Non-canonical | 553 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.00% Deletion average length | 1.15 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2396450 % of reads mapped to multiple loci | 28.19% Number of reads mapped to too many loci | 2430038 % of reads mapped to too many loci | 28.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.52% % of reads unmapped: other | 1.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2841194 2841194 2841194 N_multimapping 2396450 2396450 2396450 N_noFeature 1732835 1805924 2749637 N_ambiguous 441753 1174 498 UnstrandedReadsAssigned:1088222 PositiveStrandReadsAssigned:1455712 NegativeStrandReadsAssigned:512675 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR7472587 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR7472587-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,500,454 reads, 3,370,341 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,128 rounds 52401 SRR7472587.ke.tsv 34699 SRR7472587.se.tsv 87100 total ==> SRR7472587.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 23.9157 2.89898 Potri.005G024800.1.v4.1 1035 936 4 0.994078 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 7.94971 0.650217 Potri.016G087400.1.v4.1 270 171 3 4.08095 Potri.015G069301.1.v4.1 564 465 3 1.50074 Potri.010G195200.1.v4.1 1773 1674 1 0.138957 Potri.012G127500.1.v4.1 977 878 10 2.64937 ==> SRR7472587.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 1 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7472587 completed mapping pipeline successfully