Starting /dee2/code/volunteer_pipeline.sh SRR8846481 current disk space = 1506036121600 free memory = 1356640184 SRR8846481 SRAfilesize cc788d7aba9993f7524590b667c89da4 SRR8846481.sra SRR8846481.sra file validated SRR8846481 is single end SRR8846481 is conventional basespace SRR8846481 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846481_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.9905 34.0 33.0 34.0 28.0 34.0 2 32.8025 34.0 33.0 34.0 28.0 34.0 3 32.9395 34.0 33.0 34.0 32.0 34.0 4 33.1665 34.0 33.0 34.0 32.0 34.0 5 33.2025 34.0 33.0 34.0 32.0 34.0 6 36.72425 38.0 37.0 38.0 35.0 38.0 7 37.15925 38.0 38.0 38.0 36.0 38.0 8 37.1895 38.0 38.0 38.0 36.0 38.0 9 37.3975 38.0 38.0 38.0 37.0 38.0 10-11 37.411875 38.0 38.0 38.0 37.0 38.0 12-13 37.45125 38.0 38.0 38.0 37.0 38.0 14-15 37.457499999999996 38.0 38.0 38.0 37.0 38.0 16-17 37.404624999999996 38.0 38.0 38.0 37.0 38.0 18-19 37.509375000000006 38.0 38.0 38.0 38.0 38.0 20-21 37.35225 38.0 38.0 38.0 37.0 38.0 22-23 37.385875 38.0 38.0 38.0 37.0 38.0 24-25 37.434375 38.0 38.0 38.0 37.0 38.0 26-27 37.4985 38.0 38.0 38.0 38.0 38.0 28-29 37.359125000000006 38.0 38.0 38.0 37.0 38.0 30-31 37.36725 38.0 38.0 38.0 37.0 38.0 32-33 37.334 38.0 38.0 38.0 37.0 38.0 34-35 37.23975 38.0 38.0 38.0 36.5 38.0 36-37 37.076499999999996 38.0 38.0 38.0 36.0 38.0 38-39 37.057874999999996 38.0 38.0 38.0 36.0 38.0 40-41 36.802625 38.0 38.0 38.0 35.0 38.0 42-43 36.939375 38.0 38.0 38.0 35.5 38.0 44-45 36.94175 38.0 38.0 38.0 35.5 38.0 46-47 36.820375 38.0 38.0 38.0 35.0 38.0 48-49 36.7705 38.0 38.0 38.0 35.0 38.0 50-51 36.86987499999999 38.0 38.0 38.0 35.0 38.0 52-53 36.899 38.0 38.0 38.0 35.5 38.0 54-55 36.774625 38.0 38.0 38.0 35.0 38.0 56-57 36.359375 38.0 38.0 38.0 33.0 38.0 58-59 36.456875 38.0 38.0 38.0 33.5 38.0 60-61 36.370125 38.0 38.0 38.0 33.5 38.0 62-63 36.144625 38.0 37.5 38.0 32.5 38.0 64-65 36.0585 38.0 37.0 38.0 32.0 38.0 66-67 35.684875000000005 38.0 37.0 38.0 30.0 38.0 68-69 35.70225 38.0 37.0 38.0 30.0 38.0 70-71 35.081875 38.0 36.5 38.0 28.5 38.0 72-73 35.218125 38.0 37.0 38.0 28.5 38.0 74-75 34.83625 38.0 36.5 38.0 27.5 38.0 76-77 34.53975 38.0 36.0 38.0 26.0 38.0 78-79 33.7145 38.0 34.0 38.0 20.0 38.0 80-81 34.010125 38.0 35.0 38.0 24.5 38.0 82-83 33.405875 38.0 34.0 38.0 19.5 38.0 84-85 33.631 38.0 34.0 38.0 19.5 38.0 86-87 34.041124999999994 38.0 35.0 38.0 24.0 38.0 88-89 33.6445 38.0 34.5 38.0 19.5 38.0 90-91 33.383125 38.0 34.0 38.0 15.0 38.0 92-93 33.012625 38.0 34.0 38.0 15.0 38.0 94-95 32.65125 38.0 33.5 38.0 15.0 38.0 96-97 31.536625 38.0 32.0 38.0 8.0 38.0 98-99 29.993875 38.0 28.5 38.0 2.0 38.0 100-101 27.944499999999998 37.0 19.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 0.0 17 1.0 18 1.0 19 1.0 20 3.0 21 12.0 22 8.0 23 15.0 24 29.0 25 48.0 26 33.0 27 29.0 28 30.0 29 44.0 30 67.0 31 87.0 32 117.0 33 166.0 34 234.0 35 474.0 36 1013.0 37 1585.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.886387995712756 25.884244372990356 20.20364415862808 22.02572347266881 2 27.05 28.125 16.225 28.599999999999998 3 24.5 19.950000000000003 19.475 36.075 4 26.575 31.775 20.125 21.525 5 27.500000000000004 26.025 23.275000000000002 23.200000000000003 6 26.650000000000002 24.474999999999998 26.200000000000003 22.675 7 35.525 25.6 18.775 20.1 8 21.85 21.625 35.05 21.475 9 24.75 34.125 21.475 19.650000000000002 10-11 30.4625 25.5125 22.9875 21.0375 12-13 23.4125 23.3375 20.375 32.875 14-15 23.9125 38.3625 20.724999999999998 17.0 16-17 25.587500000000002 27.437499999999996 27.200000000000003 19.775000000000002 18-19 31.874999999999996 24.7 21.275 22.15 20-21 21.5375 30.1375 25.637500000000003 22.6875 22-23 26.375 29.525000000000002 26.974999999999998 17.125 24-25 27.9125 25.4 23.9125 22.775000000000002 26-27 31.275 28.4375 20.3375 19.950000000000003 28-29 24.1875 25.874999999999996 25.224999999999998 24.712500000000002 30-31 27.1 21.4125 31.775 19.7125 32-33 21.825 19.9875 34.362500000000004 23.825 34-35 26.5625 18.862499999999997 30.875000000000004 23.7 36-37 32.0 17.6875 31.075000000000003 19.2375 38-39 33.0 21.85 26.625 18.525 40-41 28.999999999999996 19.4875 27.9125 23.599999999999998 42-43 29.675 21.625 27.0625 21.637500000000003 44-45 37.3125 20.0875 18.6 24.0 46-47 32.9875 27.8125 17.925 21.275 48-49 29.8875 21.1375 22.6 26.375 50-51 24.587500000000002 22.125 19.037499999999998 34.25 52-53 28.1375 26.8625 14.05 30.95 54-55 28.8625 25.5625 16.4875 29.0875 56-57 27.975 27.575 13.737499999999999 30.7125 58-59 23.5 27.487499999999997 15.975 33.037499999999994 60-61 19.650000000000002 28.025 16.3375 35.9875 62-63 22.45 29.0875 15.325 33.137499999999996 64-65 18.0125 29.75 21.087500000000002 31.15 66-67 15.712499999999999 24.15 23.925 36.2125 68-69 20.4125 22.5625 21.125 35.9 70-71 20.724999999999998 21.925 27.224999999999998 30.125 72-73 18.25 21.2 28.3875 32.1625 74-75 17.6125 19.15 27.6625 35.575 76-77 21.75 15.1 33.324999999999996 29.825000000000003 78-79 18.462500000000002 12.2625 34.9125 34.362500000000004 80-81 18.5 14.099999999999998 35.5375 31.8625 82-83 18.7 13.075000000000001 40.475 27.750000000000004 84-85 19.7625 10.3125 37.8625 32.0625 86-87 21.8625 13.15 37.05 27.9375 88-89 17.275 24.224999999999998 36.6875 21.8125 90-91 16.6 29.3875 33.4 20.6125 92-93 15.462500000000002 37.512499999999996 26.700000000000003 20.325 94-95 13.9375 45.1375 25.924999999999997 15.0 96-97 10.525 53.5375 23.95 11.987499999999999 98-99 9.1875 63.849999999999994 17.4625 9.5 100-101 7.324999999999999 71.5125 14.0375 7.124999999999999 >>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 0.0 27 0.0 28 0.0 29 0.0 30 0.5 31 1.0 32 0.5 33 1.0 34 2.0 35 4.5 36 8.5 37 15.5 38 20.0 39 21.0 40 39.0 41 62.5 42 92.5 43 127.0 44 171.0 45 247.5 46 274.0 47 316.5 48 350.5 49 301.5 50 314.0 51 339.5 52 308.5 53 213.0 54 144.5 55 171.5 56 205.0 57 139.5 58 42.5 59 21.5 60 17.0 61 11.0 62 7.5 63 4.0 64 2.5 65 2.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 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 warn #Base N-Count 1 6.7 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 55.175 #Duplication Level Percentage of deduplicated Percentage of total 1 83.18985047575896 45.9 2 8.201178069777978 9.049999999999999 3 2.3561395559583147 3.9 4 1.5858631626642499 3.5000000000000004 5 1.042138649750793 2.875 6 0.5890348889895787 1.95 7 0.5437245129134572 2.1 8 0.22655188038060714 1.0 9 0.22655188038060714 1.125 >10 1.8577254191209787 19.6 >50 0.1359311282283643 6.175 >100 0.045310376076121435 2.825 >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 TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 113 2.825 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 92 2.3 RNA PCR Primer, Index 1 (100% over 22bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 82 2.0500000000000003 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 73 1.825 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 49 1.225 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 40 1.0 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 37 0.9249999999999999 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTT 35 0.8750000000000001 RNA PCR Primer, Index 11 (100% over 50bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 33 0.8250000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 33 0.8250000000000001 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 32 0.8 RNA PCR Primer, Index 1 (100% over 24bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 25 0.625 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 25 0.625 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 25bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 22 0.5499999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 21 0.525 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 21 0.525 RNA PCR Primer, Index 1 (100% over 23bp) CTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTC 21 0.525 RNA PCR Primer, Index 11 (100% over 50bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 21 0.525 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 21 0.525 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 19 0.475 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 18 0.44999999999999996 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGT 18 0.44999999999999996 RNA PCR Primer, Index 11 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 16 0.4 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTC 12 0.3 RNA PCR Primer, Index 11 (100% over 50bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 12 0.3 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 12 0.3 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 11 0.27499999999999997 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 11 0.27499999999999997 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 11 0.27499999999999997 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 10 0.25 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 10 0.25 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 10 0.25 No Hit TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 9 0.22499999999999998 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 9 0.22499999999999998 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAA 8 0.2 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 8 0.2 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 8 0.2 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCT 8 0.2 RNA PCR Primer, Index 11 (100% over 50bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit GCCCCTATCGTCTAGTGGTTCAGGACATCTCTCTTTCAAGGTGGAATTCT 7 0.17500000000000002 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TATTCTGGTGTCCTAGGCGTAGAGGATGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) TCGTGCTGAAGAGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAAT 7 0.17500000000000002 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATT 7 0.17500000000000002 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCGGCTCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 6 0.15 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 6 0.15 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CGGATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAAT 5 0.125 No Hit TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCCATCCCGATGGA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 5 0.125 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 5 0.125 No Hit GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTG 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) NGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 5 0.125 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGATGGAATTC 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTGGAA 5 0.125 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 5 0.125 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 5 0.125 No Hit >>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 0.025 0.0 0.0 0.0 2 0.0 0.025 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.05 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.05 0.0 0.0 0.0 7 0.0 0.075 0.0 0.0 0.0 8 0.0 0.075 0.0 0.0 0.0 9 0.0 0.15 0.0 0.0 0.0 10-11 0.0 0.175 0.0 0.0 0.0 12-13 0.0 0.375 0.0 0.0 0.0 14-15 0.0 0.6 0.0 0.0 0.0 16-17 0.0 1.025 0.0 0.0 0.0 18-19 0.0 1.55 0.0 0.0 0.0 20-21 0.0 2.85 0.0 0.0 0.0 22-23 0.0 6.725 0.0 0.0 0.0 24-25 0.0 13.85 0.0 0.0 0.0 26-27 0.0 22.9125 0.0 0.0 0.0 28-29 0.0 31.025 0.0 0.0 0.0 30-31 0.0 39.5625 0.0 0.0 0.0 32-33 0.0 47.1625 0.0 0.0 0.0 34-35 0.0 56.9875 0.0 0.0 0.0 36-37 0.0 67.275 0.0 0.0 0.0 38-39 0.0 73.5625 0.0 0.0 0.0 40-41 0.0 78.375 0.0 0.0 0.0 42-43 0.0 85.225 0.0 0.0 0.0 44-45 0.0 89.6125 0.0 0.0 0.0 46-47 0.0 92.025 0.0 0.0 0.0 48-49 0.0 92.625 0.0 0.0 0.0 50-51 0.0 92.8625 0.0 0.0 0.0 52-53 0.0 93.0125 0.0 0.0 0.0 54-55 0.0 93.07499999999999 0.0 0.0 0.0 56-57 0.0 93.1125 0.0 0.0 0.0 58-59 0.0 93.15 0.0 0.0 0.0 60-61 0.0 93.15 0.0 0.0 0.0 62-63 0.0 93.175 0.0 0.0 0.0 64-65 0.0 93.175 0.0 0.0 0.0 66-67 0.0 93.175 0.0 0.0 0.0 68-69 0.0 93.175 0.0 0.0 0.0 70-71 0.0 93.175 0.0 0.0 0.0 72-73 0.0 93.175 0.0 0.0 0.0 74-75 0.0 93.175 0.0 0.0 0.0 76-77 0.0 93.175 0.0 0.0 0.0 78-79 0.0 93.175 0.0 0.0 0.0 80-81 0.0 93.1875 0.0 0.0 0.0 82-83 0.0 93.2 0.0 0.0 0.0 84-85 0.0 93.225 0.0 0.0 0.0 86-87 0.0 93.225 0.0 0.0 0.0 88-89 0.0 93.225 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCTGAT 15 4.2518976E-4 104.0137 1 GTAGACC 35 2.3283064E-10 94.912506 7 AGTAGAC 35 2.3283064E-10 94.912506 6 GAGTAGA 35 2.3283064E-10 94.912506 5 CGAGTAG 35 2.3283064E-10 94.912506 4 AGACCTT 35 2.3283064E-10 94.912506 9 TCGAGTA 35 2.3283064E-10 94.912506 3 TAGACCT 35 2.3283064E-10 94.912506 8 ATGATCA 15 6.164719E-4 94.9125 9 CTGATGA 15 6.164719E-4 94.9125 3 GATGATC 15 6.164719E-4 94.9125 8 TCTGATG 15 6.164719E-4 94.9125 2 CATCGAG 40 3.1468517E-10 91.011986 1 TCCACTG 30 6.489008E-7 86.678085 1 ATCGAGT 40 6.7484507E-10 83.04844 2 CTGAGAT 35 2.777233E-8 81.35358 5 CACTGAG 35 2.777233E-8 81.35358 3 CCACTGA 35 2.777233E-8 81.35358 2 GATCCAG 35 2.777233E-8 81.35358 9 AGATCCA 35 2.777233E-8 81.35358 8 >>END_MODULE Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra Rejected 904312 READS because READLEN < 1 Read 904312 spots for SRR8846481.sra Written 904312 spots for SRR8846481.sra Rejected 904301 READS because READLEN < 1 Read 904301 spots for SRR8846481.sra Written 904301 spots for SRR8846481.sra SRR ids: ['SRR8846481.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7_xyhmeg SRR8846481.sra spots: 18086031 blocks: [[1, 904301], [904302, 1808602], [1808603, 2712903], [2712904, 3617204], [3617205, 4521505], [4521506, 5425806], [5425807, 6330107], [6330108, 7234408], [7234409, 8138709], [8138710, 9043010], [9043011, 9947311], [9947312, 10851612], [10851613, 11755913], [11755914, 12660214], [12660215, 13564515], [13564516, 14468816], [14468817, 15373117], [15373118, 16277418], [16277419, 17181719], [17181720, 18086031]] SRR8846481 file size 4340848 SRR8846481 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 SRR8846481 SRR8846481_1.fastq Input file: SRR8846481_1.fastq trimmed: SRR8846481-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 Sun Dec 8 16:41:46 2024 >> started Sun Dec 8 16:42:34 2024 >> done (47.711s) 18086031 reads processed; of these: 433 ( 0.00%) short reads filtered out after trimming by size control 56 ( 0.00%) empty reads filtered out after trimming by size control 18085542 (100.00%) reads available; of these: 3012594 (16.66%) trimmed reads available after processing 15072948 (83.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 61 0.00% 19 61 0.00% 20 62 0.00% 21 66 0.00% 22 53 0.00% 23 91 0.00% 24 102 0.00% 25 136 0.00% 26 195 0.00% 27 217 0.00% 28 250 0.00% 29 313 0.00% 30 251 0.00% 31 249 0.00% 32 255 0.00% 33 256 0.00% 34 328 0.00% 35 292 0.00% 36 315 0.00% 37 331 0.00% 38 304 0.00% 39 303 0.00% 40 343 0.00% 41 401 0.00% 42 399 0.00% 43 412 0.00% 44 447 0.00% 45 469 0.00% 46 436 0.00% 47 390 0.00% 48 397 0.00% 49 432 0.00% 50 406 0.00% 51 420 0.00% 52 449 0.00% 53 507 0.00% 54 467 0.00% 55 434 0.00% 56 547 0.00% 57 630 0.00% 58 656 0.00% 59 904 0.00% 60 1249 0.01% 61 1872 0.01% 62 2654 0.01% 63 2905 0.02% 64 4847 0.03% 65 7050 0.04% 66 15464 0.09% 67 63936 0.35% 68 85402 0.47% 69 59008 0.33% 70 51060 0.28% 71 61317 0.34% 72 25664 0.14% 73 8509 0.05% 74 10580 0.06% 75 6534 0.04% 76 5009 0.03% 77 4934 0.03% 78 5302 0.03% 79 5681 0.03% 80 5865 0.03% 81 7041 0.04% 82 9443 0.05% 83 9843 0.05% 84 10624 0.06% 85 12128 0.07% 86 13756 0.08% 87 17152 0.09% 88 22653 0.13% 89 33344 0.18% 90 46100 0.25% 91 48018 0.27% 92 58027 0.32% 93 91055 0.50% 94 110123 0.61% 95 225345 1.25% 96 284443 1.57% 97 306371 1.69% 98 455451 2.52% 99 503052 2.78% 100 299746 1.66% 101 15072948 83.34% 18085542 reads passed initial QC criterion=sequence-density sequence-density=93.13 sequence-density-rank=1 fanout-score=29.67 fanout-score-rank=1 prefix-density=93.50 prefix-fanout=29.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=93.13 sequence-density-rank=1 fanout-score=29.67 fanout-score-rank=1 prefix-density=93.50 prefix-fanout=29.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846481 - Input file: STDIN trimmed: SRR8846481-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGA -- 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 Sun Dec 8 16:45:44 2024 >> started Sun Dec 8 16:47:08 2024 >> done (84.479s) 17700743 reads processed; of these: 241228 ( 1.36%) short reads filtered out after trimming by size control 19373 ( 0.11%) empty reads filtered out after trimming by size control 17440142 (98.53%) reads available; of these: 16758050 (96.09%) trimmed reads available after processing 682092 ( 3.91%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 65542 0.38% 19 119786 0.69% 20 127770 0.73% 21 469631 2.69% 22 311624 1.79% 23 414099 2.37% 24 1427686 8.19% 25 603446 3.46% 26 707299 4.06% 27 634136 3.64% 28 898504 5.15% 29 723828 4.15% 30 746958 4.28% 31 590599 3.39% 32 779008 4.47% 33 916517 5.26% 34 999600 5.73% 35 859966 4.93% 36 1094256 6.27% 37 488351 2.80% 38 449064 2.57% 39 433504 2.49% 40 473855 2.72% 41 666213 3.82% 42 695681 3.99% 43 273872 1.57% 44 311561 1.79% 45 156723 0.90% 46 100656 0.58% 47 58012 0.33% 48 54020 0.31% 49 28453 0.16% 50 19030 0.11% 51 16875 0.10% 52 8200 0.05% 53 6123 0.04% 54 8332 0.05% 55 2341 0.01% 56 2503 0.01% 57 1563 0.01% 58 1285 0.01% 59 1222 0.01% 60 1307 0.01% 61 1992 0.01% 62 2464 0.01% 63 2625 0.02% 64 4403 0.03% 65 6540 0.04% 66 14702 0.08% 67 62099 0.36% 68 82866 0.48% 69 57005 0.33% 70 49372 0.28% 71 59050 0.34% 72 22425 0.13% 73 5429 0.03% 74 3118 0.02% 75 2256 0.01% 76 2508 0.01% 77 4884 0.03% 78 2631 0.02% 79 2681 0.02% 80 3896 0.02% 81 2950 0.02% 82 2676 0.02% 83 3587 0.02% 84 1937 0.01% 85 1867 0.01% 86 1909 0.01% 87 1498 0.01% 88 1248 0.01% 89 1520 0.01% 90 1347 0.01% 91 1361 0.01% 92 1339 0.01% 93 1673 0.01% 94 1662 0.01% 95 2313 0.01% 96 3460 0.02% 97 4406 0.03% 98 6416 0.04% 99 8482 0.05% 100 11130 0.06% 101 235414 1.35% criterion=sequence-density sequence-density=3.48 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=17.84 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=1.0 sequence=AAGGAGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCA Started job on | Dec 08 16:49:37 Started mapping on | Dec 08 16:49:37 Finished on | Dec 08 16:59:16 Mapping speed, Million of reads per hour | 110.83 Number of input reads | 17824941 Average input read length | 35 UNIQUE READS: Uniquely mapped reads number | 2473262 Uniquely mapped reads % | 13.88% Average mapped length | 29.21 Number of splices: Total | 36680 Number of splices: Annotated (sjdb) | 24862 Number of splices: GT/AG | 33960 Number of splices: GC/AG | 1669 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 1033 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6810102 % of reads mapped to multiple loci | 38.21% Number of reads mapped to too many loci | 7252787 % of reads mapped to too many loci | 40.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.78% % of reads unmapped: other | 0.45% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8541577 8541577 8541577 N_multimapping 6810102 6810102 6810102 N_noFeature 1349332 1596844 2212690 N_ambiguous 44652 31287 521 UnstrandedReadsAssigned:1079278 PositiveStrandReadsAssigned:845131 NegativeStrandReadsAssigned:260051 Dataset is classified unstranded MeadianReadLen=33 20thPercentileLength=25 echo kmer=21 SRR8846481 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=21 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 21 [index] number of targets: 52,972 [index] number of k-mers: 65,978,135 [index] number of equivalence classes: 190,841 [quant] running in single-end mode [quant] will process file 1: SRR8846481-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,824,941 reads, 3,950,654 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 939 rounds 52973 SRR8846481.ke.tsv 35125 SRR8846481.se.tsv 88098 total ==> SRR8846481.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 3 0.469537 PNS24243 293 194 0 0 KQK14069 1603 1504 22.061 3.14977 KQK14071 474 375 0 0 ==> SRR8846481.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 2 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 28 BRADI_1g74790v3 27 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 1 SRR8846481 completed mapping pipeline successfully