Starting /dee2/code/volunteer_pipeline.sh SRR8846536 current disk space = 1531615899648 free memory = 1377033816 SRR8846536 SRAfilesize b42d473a3559708c8b75bfc078451c8e SRR8846536.sra SRR8846536.sra file validated SRR8846536 is single end SRR8846536 is conventional basespace SRR8846536 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846536_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.8475 34.0 33.0 34.0 27.0 34.0 2 32.796 34.0 33.0 34.0 28.0 34.0 3 32.904 34.0 33.0 34.0 31.0 34.0 4 32.9475 34.0 33.0 34.0 32.0 34.0 5 32.93475 34.0 33.0 34.0 32.0 34.0 6 36.50925 38.0 37.0 38.0 34.0 38.0 7 37.1205 38.0 38.0 38.0 36.0 38.0 8 37.2975 38.0 38.0 38.0 36.0 38.0 9 37.28375 38.0 38.0 38.0 37.0 38.0 10-11 37.466375 38.0 38.0 38.0 37.0 38.0 12-13 37.486375 38.0 38.0 38.0 37.5 38.0 14-15 37.4765 38.0 38.0 38.0 37.0 38.0 16-17 37.421875 38.0 38.0 38.0 37.0 38.0 18-19 37.485875 38.0 38.0 38.0 37.0 38.0 20-21 37.4765 38.0 38.0 38.0 37.0 38.0 22-23 37.33725 38.0 38.0 38.0 37.0 38.0 24-25 37.3885 38.0 38.0 38.0 37.0 38.0 26-27 37.490875 38.0 38.0 38.0 37.5 38.0 28-29 37.466875 38.0 38.0 38.0 37.5 38.0 30-31 37.442499999999995 38.0 38.0 38.0 37.5 38.0 32-33 37.340500000000006 38.0 38.0 38.0 37.0 38.0 34-35 37.131 38.0 38.0 38.0 36.5 38.0 36-37 37.074125 38.0 38.0 38.0 36.5 38.0 38-39 37.095625 38.0 38.0 38.0 36.5 38.0 40-41 37.047250000000005 38.0 38.0 38.0 36.0 38.0 42-43 37.018874999999994 38.0 38.0 38.0 36.5 38.0 44-45 37.088375 38.0 38.0 38.0 36.0 38.0 46-47 37.082750000000004 38.0 38.0 38.0 36.0 38.0 48-49 37.193625 38.0 38.0 38.0 36.5 38.0 50-51 37.30075 38.0 38.0 38.0 37.0 38.0 52-53 37.31075 38.0 38.0 38.0 37.0 38.0 54-55 37.1485 38.0 38.0 38.0 36.5 38.0 56-57 36.965875 38.0 38.0 38.0 36.0 38.0 58-59 36.832499999999996 38.0 38.0 38.0 35.5 38.0 60-61 36.7735 38.0 38.0 38.0 35.0 38.0 62-63 36.2875 38.0 38.0 38.0 33.0 38.0 64-65 36.396 38.0 37.5 38.0 33.5 38.0 66-67 36.2635 38.0 37.0 38.0 33.0 38.0 68-69 36.052625 38.0 37.0 38.0 32.0 38.0 70-71 36.127624999999995 38.0 37.0 38.0 33.0 38.0 72-73 36.03375 38.0 37.0 38.0 32.5 38.0 74-75 35.77125 38.0 37.0 38.0 31.0 38.0 76-77 35.51575 38.0 37.0 38.0 30.0 38.0 78-79 35.373000000000005 38.0 37.0 38.0 28.5 38.0 80-81 35.3595 38.0 37.0 38.0 28.5 38.0 82-83 35.2605 38.0 37.0 38.0 28.5 38.0 84-85 35.441375 38.0 37.0 38.0 29.0 38.0 86-87 35.66375 38.0 37.0 38.0 31.5 38.0 88-89 35.5035 38.0 37.0 38.0 31.0 38.0 90-91 35.097 38.0 37.0 38.0 30.0 38.0 92-93 34.570499999999996 38.0 37.0 38.0 27.5 38.0 94-95 33.3635 38.0 36.0 38.0 14.5 38.0 96-97 30.80625 38.0 32.5 38.0 2.0 38.0 98-99 27.784125 38.0 13.5 38.0 2.0 38.0 100-101 24.909625 36.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 1.0 15 0.0 16 0.0 17 0.0 18 1.0 19 0.0 20 0.0 21 4.0 22 4.0 23 3.0 24 19.0 25 32.0 26 24.0 27 22.0 28 21.0 29 43.0 30 51.0 31 59.0 32 115.0 33 168.0 34 286.0 35 528.0 36 801.0 37 1817.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.30107526881721 24.43548387096774 21.478494623655912 19.78494623655914 2 26.450000000000003 28.175 18.224999999999998 27.150000000000002 3 28.349999999999998 19.675 19.05 32.925 4 27.325 34.699999999999996 15.45 22.525000000000002 5 26.075 28.025 22.575 23.325000000000003 6 25.75 24.55 25.55 24.15 7 37.675 25.45 16.6 20.275000000000002 8 19.225 21.55 36.55 22.675 9 23.425 35.675000000000004 21.95 18.95 10-11 30.4875 22.75 25.95 20.8125 12-13 22.0625 21.0625 24.425 32.45 14-15 22.900000000000002 36.987500000000004 21.925 18.1875 16-17 23.275000000000002 26.924999999999997 31.974999999999998 17.825 18-19 33.4375 22.8375 21.7375 21.987499999999997 20-21 22.475 27.987499999999997 26.8 22.7375 22-23 28.475 28.749999999999996 28.175 14.6 24-25 28.237499999999997 26.8 26.987499999999997 17.974999999999998 26-27 29.4125 27.950000000000003 24.6625 17.974999999999998 28-29 22.775000000000002 26.224999999999998 27.5625 23.4375 30-31 26.887499999999996 19.3 33.825 19.9875 32-33 26.900000000000002 16.2375 33.0625 23.799999999999997 34-35 33.5 15.3375 29.312500000000004 21.85 36-37 37.25 16.2125 26.5375 20.0 38-39 33.875 19.7625 25.4 20.962500000000002 40-41 29.5875 19.825 23.0125 27.575 42-43 31.937500000000004 24.462500000000002 18.675 24.925 44-45 37.762499999999996 23.9 13.6625 24.675 46-47 30.112499999999997 28.175 16.2625 25.45 48-49 25.124999999999996 26.700000000000003 16.7125 31.4625 50-51 22.275 27.537499999999998 15.35 34.8375 52-53 23.75 33.1 12.6375 30.5125 54-55 19.9625 32.1375 16.6375 31.2625 56-57 19.900000000000002 30.85 17.9 31.35 58-59 16.525000000000002 33.7625 19.75 29.9625 60-61 19.15 32.875 17.2625 30.7125 62-63 20.724999999999998 27.450000000000003 21.525 30.3 64-65 17.5625 29.549999999999997 25.575 27.3125 66-67 17.45 25.424999999999997 27.0125 30.112499999999997 68-69 22.1375 23.8875 26.724999999999998 27.250000000000004 70-71 23.2375 22.6 28.675 25.4875 72-73 24.3 18.099999999999998 28.762500000000003 28.8375 74-75 18.6125 13.750000000000002 31.974999999999998 35.6625 76-77 20.2125 10.6375 39.537499999999994 29.612500000000004 78-79 20.3625 8.825 39.0 31.8125 80-81 20.05 10.5 38.0875 31.362499999999997 82-83 21.0125 10.612499999999999 41.699999999999996 26.674999999999997 84-85 21.05 14.5375 36.175000000000004 28.237499999999997 86-87 19.2 23.3625 33.9875 23.45 88-89 13.850000000000001 37.724999999999994 32.5125 15.9125 90-91 12.1375 47.612500000000004 25.5625 14.6875 92-93 11.5875 57.137499999999996 19.112499999999997 12.1625 94-95 9.2125 65.8 17.5125 7.475 96-97 7.324999999999999 75.41250000000001 12.174999999999999 5.0874999999999995 98-99 5.3 83.0875 7.9125 3.6999999999999997 100-101 3.45 86.7625 5.7875000000000005 4.0 >>END_MODULE >>Per sequence GC content pass #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 0.0 31 0.5 32 2.0 33 2.5 34 5.0 35 8.5 36 10.0 37 12.0 38 15.5 39 43.0 40 78.5 41 145.5 42 201.0 43 230.0 44 331.0 45 369.5 46 404.5 47 423.0 48 339.0 49 289.5 50 283.5 51 256.5 52 168.0 53 93.5 54 72.0 55 98.5 56 72.0 57 19.0 58 13.0 59 5.5 60 3.5 61 2.0 62 1.5 63 1.0 64 0.0 65 0.0 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 7.000000000000001 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 57.825 #Duplication Level Percentage of deduplicated Percentage of total 1 85.21400778210116 49.275000000000006 2 6.571552096843926 7.6 3 2.3346303501945527 4.05 4 1.3834846519671422 3.2 5 1.1673151750972763 3.375 6 0.6917423259835711 2.4 7 0.4755728491137051 1.925 8 0.3026372676178124 1.4000000000000001 9 0.08646779074794639 0.44999999999999996 >10 1.5131863380890618 15.325 >50 0.25940337224383914 11.0 >100 0.0 0.0 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 100 2.5 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 83 2.075 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 75 1.875 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 67 1.675 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 61 1.525 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 54 1.35 RNA PCR Primer, Index 1 (100% over 24bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 47 1.175 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 43 1.075 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 26 0.65 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 26 0.65 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 25 0.625 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 25 0.625 RNA PCR Primer, Index 1 (100% over 25bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 25 0.625 RNA PCR Primer, Index 1 (100% over 24bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 19 0.475 RNA PCR Primer, Index 1 (100% over 29bp) TCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTT 18 0.44999999999999996 RNA PCR Primer, Index 26 (100% over 50bp) CTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTC 17 0.42500000000000004 RNA PCR Primer, Index 26 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 16 0.4 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 15 0.375 RNA PCR Primer, Index 1 (100% over 24bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 28bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 13 0.325 RNA PCR Primer, Index 1 (100% over 31bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 13 0.325 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 11 0.27499999999999997 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 10 0.25 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 10 0.25 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 10 0.25 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 10 0.25 RNA PCR Primer, Index 1 (100% over 27bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGT 8 0.2 RNA PCR Primer, Index 26 (100% over 50bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 8 0.2 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) TCCGTCGTAGTCTAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 34bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 7 0.17500000000000002 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 6 0.15 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 6 0.15 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 6 0.15 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 6 0.15 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCT 6 0.15 RNA PCR Primer, Index 26 (100% over 50bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CTTAGCGGATACTATGATAGCACCTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) GACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 5 0.125 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit CGACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) NATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCA 5 0.125 No Hit GGGGATGTAGCTCAGATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) CGACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GCACCAGTGGTCTAGTGGTAGAATATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 5 0.125 No Hit TATTCTGGTGTCCTAGGCGTAGAGGATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 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 0.05 0.0 0.0 0.0 2 0.0 0.05 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 0.075 0.0 0.0 0.0 7 0.0 0.1 0.0 0.0 0.0 8 0.0 0.15 0.0 0.0 0.0 9 0.0 0.2 0.0 0.0 0.0 10-11 0.0 0.3 0.0 0.0 0.0 12-13 0.0 0.4625 0.0 0.0 0.0 14-15 0.0 0.7625 0.0 0.0 0.0 16-17 0.0 1.9875 0.0 0.0 0.0 18-19 0.0 3.8 0.0 0.0 0.0 20-21 0.0 7.5 0.0 0.0 0.0 22-23 0.0 17.375 0.0 0.0 0.0 24-25 0.0 28.6375 0.0 0.0 0.0 26-27 0.0 40.625 0.0 0.0 0.0 28-29 0.0 51.25 0.0 0.0 0.0 30-31 0.0 60.375 0.0 0.0 0.0 32-33 0.0 69.375 0.0 0.0 0.0 34-35 0.0 80.07499999999999 0.0 0.0 0.0 36-37 0.0 87.35 0.0 0.0 0.0 38-39 0.0 90.82499999999999 0.0 0.0 0.0 40-41 0.0 92.4875 0.0 0.0 0.0 42-43 0.0 94.30000000000001 0.0 0.0 0.0 44-45 0.0 95.025 0.0 0.0 0.0 46-47 0.0 95.36250000000001 0.0 0.0 0.0 48-49 0.0 95.4125 0.0 0.0 0.0 50-51 0.0 95.425 0.0 0.0 0.0 52-53 0.0 95.425 0.0 0.0 0.0 54-55 0.0 95.425 0.0 0.0 0.0 56-57 0.0 95.425 0.0 0.0 0.0 58-59 0.0 95.425 0.0 0.0 0.0 60-61 0.0 95.425 0.0 0.0 0.0 62-63 0.0 95.425 0.0 0.0 0.0 64-65 0.0 95.425 0.0 0.0 0.0 66-67 0.0 95.425 0.0 0.0 0.0 68-69 0.0 95.425 0.0 0.0 0.0 70-71 0.0 95.425 0.0 0.0 0.0 72-73 0.0 95.425 0.0 0.0 0.0 74-75 0.0 95.425 0.0 0.0 0.0 76-77 0.0 95.425 0.0 0.0 0.0 78-79 0.0 95.425 0.0 0.0 0.0 80-81 0.0 95.425 0.0 0.0 0.0 82-83 0.0 95.425 0.0 0.0 0.0 84-85 0.0 95.425 0.0 0.0 0.0 86-87 0.0 95.425 0.0 0.0 0.0 88-89 0.0 95.425 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAATTCA 15 4.7401295E-4 101.26666 1 GGGATTG 30 5.9571903E-9 101.26666 1 CATGATC 15 6.1582687E-4 94.9375 6 TTGTAGT 35 2.3283064E-10 94.9375 5 AATTCAT 15 6.1582687E-4 94.9375 2 ATGATCT 15 6.1582687E-4 94.9375 7 TGATCTG 15 6.1582687E-4 94.9375 8 GATTGTA 30 9.502401E-9 94.9375 3 TAGTTCA 35 2.3283064E-10 94.9375 8 ATTGTAG 30 9.502401E-9 94.9375 4 GATCTGG 15 6.1582687E-4 94.9375 9 TGTAGTT 30 9.502401E-9 94.9375 6 AGTTCAA 35 2.3283064E-10 94.9375 9 GTAGTTC 35 2.3283064E-10 94.9375 7 GACACGA 40 4.3939508E-8 75.950005 1 TTCATGA 20 0.0019308104 71.203125 4 GGATTGT 40 7.000381E-8 71.203125 2 ATTCATG 20 0.0019308104 71.203125 3 ACACGAC 45 1.5831938E-7 63.291664 2 TCATGAT 25 0.004676345 56.962505 5 >>END_MODULE Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958760 READS because READLEN < 1 Read 958760 spots for SRR8846536.sra Written 958760 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra Rejected 958757 READS because READLEN < 1 Read 958757 spots for SRR8846536.sra Written 958757 spots for SRR8846536.sra SRR ids: ['SRR8846536.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9l4u52d6 SRR8846536.sra spots: 19175143 blocks: [[1, 958757], [958758, 1917514], [1917515, 2876271], [2876272, 3835028], [3835029, 4793785], [4793786, 5752542], [5752543, 6711299], [6711300, 7670056], [7670057, 8628813], [8628814, 9587570], [9587571, 10546327], [10546328, 11505084], [11505085, 12463841], [12463842, 13422598], [13422599, 14381355], [14381356, 15340112], [15340113, 16298869], [16298870, 17257626], [17257627, 18216383], [18216384, 19175143]] SRR8846536 file size 4603553 SRR8846536 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 SRR8846536 SRR8846536_1.fastq Input file: SRR8846536_1.fastq trimmed: SRR8846536-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 Mon Dec 9 08:24:49 2024 >> started Mon Dec 9 08:25:37 2024 >> done (47.379s) 19175143 reads processed; of these: 312 ( 0.00%) short reads filtered out after trimming by size control 37 ( 0.00%) empty reads filtered out after trimming by size control 19174794 (100.00%) reads available; of these: 4928852 (25.70%) trimmed reads available after processing 14245942 (74.30%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 41 0.00% 19 35 0.00% 20 49 0.00% 21 40 0.00% 22 57 0.00% 23 60 0.00% 24 74 0.00% 25 94 0.00% 26 136 0.00% 27 176 0.00% 28 241 0.00% 29 287 0.00% 30 290 0.00% 31 257 0.00% 32 191 0.00% 33 184 0.00% 34 155 0.00% 35 136 0.00% 36 165 0.00% 37 114 0.00% 38 132 0.00% 39 163 0.00% 40 141 0.00% 41 170 0.00% 42 227 0.00% 43 253 0.00% 44 271 0.00% 45 292 0.00% 46 210 0.00% 47 181 0.00% 48 152 0.00% 49 148 0.00% 50 123 0.00% 51 138 0.00% 52 152 0.00% 53 175 0.00% 54 194 0.00% 55 202 0.00% 56 229 0.00% 57 267 0.00% 58 300 0.00% 59 464 0.00% 60 537 0.00% 61 878 0.00% 62 1055 0.01% 63 1611 0.01% 64 2505 0.01% 65 2993 0.02% 66 7917 0.04% 67 36083 0.19% 68 38809 0.20% 69 29455 0.15% 70 24072 0.13% 71 28613 0.15% 72 12360 0.06% 73 4346 0.02% 74 5242 0.03% 75 3751 0.02% 76 3426 0.02% 77 3347 0.02% 78 4171 0.02% 79 4651 0.02% 80 5729 0.03% 81 7978 0.04% 82 13678 0.07% 83 13259 0.07% 84 12622 0.07% 85 14285 0.07% 86 19329 0.10% 87 29579 0.15% 88 52304 0.27% 89 81576 0.43% 90 124551 0.65% 91 136028 0.71% 92 167362 0.87% 93 262991 1.37% 94 305112 1.59% 95 566736 2.96% 96 656722 3.42% 97 571571 2.98% 98 679871 3.55% 99 595936 3.11% 100 388445 2.03% 101 14245942 74.30% 19174794 reads passed initial QC criterion=sequence-density sequence-density=95.31 sequence-density-rank=1 fanout-score=34.74 fanout-score-rank=1 prefix-density=95.83 prefix-fanout=34.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=95.31 sequence-density-rank=1 fanout-score=34.74 fanout-score-rank=1 prefix-density=95.83 prefix-fanout=34.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846536 - Input file: STDIN trimmed: SRR8846536-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 Mon Dec 9 08:27:15 2024 >> started Mon Dec 9 08:28:48 2024 >> done (93.725s) 18775319 reads processed; of these: 677826 ( 3.61%) short reads filtered out after trimming by size control 7897 ( 0.04%) empty reads filtered out after trimming by size control 18089596 (96.35%) reads available; of these: 17693489 (97.81%) trimmed reads available after processing 396107 ( 2.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 231050 1.28% 19 420318 2.32% 20 412368 2.28% 21 1338772 7.40% 22 719306 3.98% 23 802552 4.44% 24 1937620 10.71% 25 870525 4.81% 26 1022799 5.65% 27 896494 4.96% 28 1023716 5.66% 29 800518 4.43% 30 993288 5.49% 31 641017 3.54% 32 1079882 5.97% 33 963538 5.33% 34 876259 4.84% 35 674830 3.73% 36 713853 3.95% 37 274984 1.52% 38 212384 1.17% 39 176946 0.98% 40 152802 0.84% 41 150511 0.83% 42 150382 0.83% 43 57611 0.32% 44 48324 0.27% 45 21594 0.12% 46 10521 0.06% 47 5334 0.03% 48 4449 0.02% 49 2701 0.01% 50 1762 0.01% 51 1594 0.01% 52 943 0.01% 53 696 0.00% 54 756 0.00% 55 277 0.00% 56 340 0.00% 57 204 0.00% 58 224 0.00% 59 337 0.00% 60 399 0.00% 61 715 0.00% 62 845 0.00% 63 1394 0.01% 64 2221 0.01% 65 2656 0.01% 66 7464 0.04% 67 34978 0.19% 68 37506 0.21% 69 28244 0.16% 70 22972 0.13% 71 27246 0.15% 72 10702 0.06% 73 2703 0.01% 74 1850 0.01% 75 1396 0.01% 76 1392 0.01% 77 1557 0.01% 78 1541 0.01% 79 1398 0.01% 80 1618 0.01% 81 1436 0.01% 82 1184 0.01% 83 1381 0.01% 84 971 0.01% 85 934 0.01% 86 887 0.00% 87 843 0.00% 88 834 0.00% 89 834 0.00% 90 885 0.00% 91 922 0.01% 92 1050 0.01% 93 1336 0.01% 94 1408 0.01% 95 1801 0.01% 96 2604 0.01% 97 3428 0.02% 98 5144 0.03% 99 5128 0.03% 100 6726 0.04% 101 164682 0.91% criterion=sequence-density sequence-density=4.27 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGA criterion=fanout-score sequence-density=0.36 sequence-density-rank=13 fanout-score=15.65 fanout-score-rank=1 prefix-density=5.57 prefix-fanout=1.0 sequence=GAGCACCGCCCTGTCAAGG Started job on | Dec 09 08:30:26 Started mapping on | Dec 09 08:30:27 Finished on | Dec 09 08:35:39 Mapping speed, Million of reads per hour | 213.34 Number of input reads | 18489071 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 2865825 Uniquely mapped reads % | 15.50% Average mapped length | 26.21 Number of splices: Total | 38008 Number of splices: Annotated (sjdb) | 22220 Number of splices: GT/AG | 34848 Number of splices: GC/AG | 2652 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 490 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7320274 % of reads mapped to multiple loci | 39.59% Number of reads mapped to too many loci | 7236072 % of reads mapped to too many loci | 39.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.27% % of reads unmapped: other | 0.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8302972 8302972 8302972 N_multimapping 7320274 7320274 7320274 N_noFeature 1662949 1839646 2670093 N_ambiguous 49230 29724 621 UnstrandedReadsAssigned:1153646 PositiveStrandReadsAssigned:996455 NegativeStrandReadsAssigned:195111 Dataset is classified positive stranded MeadianReadLen=28 20thPercentileLength=23 echo kmer=19 SRR8846536 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: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR8846536-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,489,071 reads, 3,262,195 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,011 rounds 52973 SRR8846536.ke.tsv 35125 SRR8846536.se.tsv 88098 total ==> SRR8846536.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 6 1.63941 PNS24243 293 194 0 0 KQK14069 1603 1504 229.182 57.1247 KQK14071 474 375 0 0 ==> SRR8846536.se.tsv <== BRADI_1g14170v3 274 BRADI_1g53295v3 3 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 35 BRADI_1g74790v3 26 BRADI_1g09890v3 0 BRADI_1g77505v3 6 BRADI_1g48960v3 0 SRR8846536 completed mapping pipeline successfully