Starting /dee2/code/volunteer_pipeline.sh SRR6941583 current disk space = 1551432118272 free memory = 1599734672 SRR6941583 SRAfilesize fc1d0aca48aabd8c2a118d5f0be67f3b SRR6941583.sra SRR6941583.sra file validated SRR6941583 is single end SRR6941583 is conventional basespace SRR6941583 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941583_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.13825 34.0 33.0 34.0 32.0 34.0 2 33.25625 34.0 33.0 34.0 32.0 34.0 3 32.68425 34.0 33.0 34.0 30.0 34.0 4 33.13075 34.0 33.0 34.0 32.0 34.0 5 33.15725 34.0 33.0 34.0 31.0 34.0 6 36.94175 38.0 37.0 38.0 36.0 38.0 7 37.31575 38.0 38.0 38.0 37.0 38.0 8 37.5425 38.0 38.0 38.0 37.0 38.0 9 37.55675 38.0 38.0 38.0 37.0 38.0 10-11 37.4795 38.0 38.0 38.0 37.0 38.0 12-13 37.431125 38.0 38.0 38.0 37.0 38.0 14-15 37.4405 38.0 38.0 38.0 37.0 38.0 16-17 36.258624999999995 38.0 37.5 38.0 32.0 38.0 18-19 36.933125000000004 38.0 38.0 38.0 34.5 38.0 20-21 35.8855 38.0 37.5 38.0 29.5 38.0 22-23 37.060125 38.0 38.0 38.0 35.5 38.0 24-25 37.379125 38.0 38.0 38.0 37.0 38.0 26-27 37.304625 38.0 38.0 38.0 37.0 38.0 28-29 37.37875 38.0 38.0 38.0 37.0 38.0 30-31 37.345875 38.0 38.0 38.0 37.0 38.0 32-33 37.191374999999994 38.0 38.0 38.0 36.5 38.0 34-35 37.02975 38.0 38.0 38.0 36.5 38.0 36-37 36.947 38.0 38.0 38.0 36.0 38.0 38-39 36.9925 38.0 38.0 38.0 36.0 38.0 40-41 36.98775 38.0 38.0 38.0 36.0 38.0 42-43 36.900625000000005 38.0 38.0 38.0 35.5 38.0 44-45 36.747749999999996 38.0 38.0 38.0 35.0 38.0 46-47 36.560375 38.0 38.0 38.0 34.0 38.0 48-49 36.803375 38.0 38.0 38.0 35.0 38.0 50-51 36.515375 38.0 38.0 38.0 34.0 38.0 52-53 36.383750000000006 38.0 38.0 38.0 33.5 38.0 54-55 36.711749999999995 38.0 38.0 38.0 34.5 38.0 56-57 36.6845 38.0 38.0 38.0 34.5 38.0 58-59 36.767250000000004 38.0 38.0 38.0 35.0 38.0 60-61 36.691125 38.0 38.0 38.0 35.0 38.0 62-63 35.931125 38.0 37.0 38.0 31.0 38.0 64-65 35.15712499999999 38.0 36.5 38.0 28.0 38.0 66-67 34.741375000000005 38.0 35.0 38.0 21.5 38.0 68-69 35.3955 38.0 37.0 38.0 28.5 38.0 70-71 34.714124999999996 38.0 35.5 38.0 26.0 38.0 72-73 33.90575 38.0 33.5 38.0 20.0 38.0 74-75 33.35525 37.5 33.0 38.0 15.0 38.0 76-77 33.8245 37.5 33.5 38.0 24.5 38.0 78-79 33.813625 37.5 33.5 38.0 24.5 38.0 80-81 34.271 37.5 34.0 38.0 25.0 38.0 82-83 33.72525 37.0 33.5 38.0 20.0 38.0 84-85 33.415875 37.0 33.0 38.0 19.5 38.0 86-87 33.604875 37.5 33.5 38.0 15.0 38.0 88-89 34.533874999999995 38.0 34.5 38.0 26.0 38.0 90-91 34.926874999999995 38.0 35.0 38.0 27.0 38.0 92-93 34.903375 38.0 36.0 38.0 27.0 38.0 94-95 35.242125 38.0 37.0 38.0 29.0 38.0 96-97 34.072625 38.0 35.5 38.0 24.5 38.0 98-99 32.345875 38.0 34.0 38.0 8.5 38.0 100-101 29.785375000000002 38.0 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 1.0 12 0.0 13 0.0 14 2.0 15 0.0 16 1.0 17 0.0 18 0.0 19 3.0 20 0.0 21 2.0 22 7.0 23 6.0 24 9.0 25 14.0 26 12.0 27 21.0 28 34.0 29 42.0 30 66.0 31 68.0 32 120.0 33 180.0 34 331.0 35 650.0 36 1304.0 37 1126.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.800000000000004 24.075 16.900000000000002 26.224999999999998 2 30.207551887971995 32.38309577394349 18.504626156539132 18.904726181545385 3 31.275 19.825 26.75 22.15 4 27.925 30.5 13.4 28.175 5 39.75 18.575 21.375 20.3 6 20.1 38.2 22.900000000000002 18.8 7 43.025000000000006 21.275 20.575 15.125 8 21.2 17.724999999999998 42.875 18.2 9 18.075 43.25 18.2 20.474999999999998 10-11 36.2375 27.8875 19.2625 16.6125 12-13 17.0 17.375 22.45 43.175000000000004 14-15 20.2125 38.1625 26.437500000000004 15.187500000000002 16-17 26.887499999999996 17.6625 40.637499999999996 14.8125 18-19 38.625 22.3125 24.825 14.2375 20-21 14.374999999999998 27.450000000000003 36.6375 21.5375 22-23 32.6625 27.762500000000003 23.5375 16.037499999999998 24-25 31.8625 28.999999999999996 25.0375 14.099999999999998 26-27 40.5625 26.0 19.037499999999998 14.399999999999999 28-29 15.225 40.2625 23.275000000000002 21.2375 30-31 19.85 9.762500000000001 47.5625 22.825 32-33 32.1125 11.525 28.199999999999996 28.1625 34-35 37.075 21.475 24.9125 16.537499999999998 36-37 43.3375 17.2375 27.500000000000004 11.924999999999999 38-39 23.9125 18.3 34.9875 22.8 40-41 23.35 15.6375 21.675 39.3375 42-43 36.025 27.900000000000002 16.9375 19.1375 44-45 53.05 15.275 14.124999999999998 17.549999999999997 46-47 26.8 29.7375 15.462500000000002 28.000000000000004 48-49 19.6125 26.1125 18.0 36.275 50-51 28.050000000000004 24.825 7.95 39.175 52-53 27.55 44.5125 7.062499999999999 20.875 54-55 16.7625 25.4625 21.4875 36.2875 56-57 12.962499999999999 29.95 12.675 44.4125 58-59 22.575 22.025 16.45 38.95 60-61 15.387500000000001 28.349999999999998 24.675 31.587500000000002 62-63 21.1375 21.4375 17.724999999999998 39.7 64-65 16.075 23.3875 27.737499999999997 32.800000000000004 66-67 15.137500000000001 18.387500000000003 27.925 38.550000000000004 68-69 28.875 18.45 20.3625 32.3125 70-71 18.3125 27.825 32.324999999999996 21.5375 72-73 24.325 14.787500000000001 31.974999999999998 28.9125 74-75 19.2625 9.225 27.8125 43.7 76-77 20.7 12.025 44.6 22.675 78-79 19.787499999999998 8.475000000000001 41.875 29.862499999999997 80-81 20.1 9.4625 34.675 35.7625 82-83 28.125 6.9125000000000005 39.675 25.2875 84-85 19.075 8.5875 38.45 33.887499999999996 86-87 18.912499999999998 17.549999999999997 40.362500000000004 23.175 88-89 13.0375 39.025 30.9625 16.975 90-91 8.9 43.275000000000006 30.162499999999998 17.6625 92-93 16.3875 49.3625 22.5125 11.737499999999999 94-95 9.762500000000001 66.5 17.1875 6.550000000000001 96-97 7.825 80.33749999999999 9.625 2.2125 98-99 3.5749999999999997 92.525 3.05 0.8500000000000001 100-101 1.0250000000000001 96.55 1.575 0.8500000000000001 >>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 0.0 31 0.0 32 0.5 33 2.0 34 1.5 35 1.0 36 5.0 37 5.0 38 1.0 39 2.5 40 13.5 41 27.5 42 59.5 43 152.0 44 264.0 45 510.5 46 586.5 47 419.5 48 384.0 49 300.0 50 180.5 51 227.0 52 305.0 53 261.0 54 133.0 55 44.5 56 40.0 57 30.0 58 12.5 59 13.0 60 11.0 61 3.5 62 2.0 63 0.5 64 0.0 65 0.0 66 0.5 67 0.5 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 pass #Base N-Count 1 0.0 2 0.025 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 50.724999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 89.15722030556925 45.225 2 4.2878265155248885 4.35 3 1.4785608674223756 2.25 4 1.1828486939379004 2.4 5 0.5421389847215378 1.375 6 0.4928536224741252 1.5 7 0.4928536224741252 1.7500000000000002 8 0.14785608674223755 0.6 9 0.2957121734844751 1.35 >10 1.3799901429275505 13.775 >50 0.2957121734844751 9.675 >100 0.2464268112370626 15.75 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 157 3.925 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 132 3.3000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 129 3.225 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 109 2.725 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 103 2.5749999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 91 2.275 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 66 1.6500000000000001 RNA PCR Primer, Index 1 (100% over 29bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 65 1.625 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 57 1.425 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 55 1.375 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 53 1.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 41 1.0250000000000001 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 39 0.975 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 35 0.8750000000000001 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 30 0.75 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 30 0.75 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 30 0.75 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 22 0.5499999999999999 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 18 0.44999999999999996 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 18 0.44999999999999996 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 22bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 29bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 16 0.4 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 16 0.4 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 14 0.35000000000000003 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 13 0.325 RNA PCR Primer, Index 1 (100% over 29bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 33bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 25bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 8 0.2 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 8 0.2 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 7 0.17500000000000002 No Hit ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 31bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGC 7 0.17500000000000002 RNA PCR Primer, Index 22 (100% over 50bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CACGACTCTCGGCAACGGATATCTCGGCTCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) GGCGGATGTAGCCAAGTGGTTCAAGGCAGTGGATTTGGAATTCTCGGGTG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 6 0.15 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 5 0.125 No Hit GCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit AACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 5 0.125 RNA PCR Primer, Index 2 (100% over 34bp) GGTAGTTCGACCGCGGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 5 0.125 No Hit AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GGGATTGTAGTTCAATTGGTGAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TGAACCTTGGGGAAAAGCCGCCTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) >>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 0.225 0.0 0.0 0.0 2 0.0 0.225 0.0 0.0 0.0 3 0.0 0.225 0.0 0.0 0.0 4 0.0 0.225 0.0 0.0 0.0 5 0.0 0.225 0.0 0.0 0.0 6 0.0 0.225 0.0 0.0 0.0 7 0.0 0.25 0.0 0.0 0.0 8 0.0 0.275 0.0 0.0 0.0 9 0.0 0.275 0.0 0.0 0.0 10-11 0.0 0.275 0.0 0.0 0.0 12-13 0.0 0.30000000000000004 0.0 0.0 0.0 14-15 0.0 0.38749999999999996 0.0 0.0 0.0 16-17 0.0 0.825 0.0 0.0 0.0 18-19 0.0 1.6875 0.0 0.0 0.0 20-21 0.0 3.2 0.0 0.0 0.0 22-23 0.0 11.9625 0.0 0.0 0.0 24-25 0.0 26.862499999999997 0.0 0.0 0.0 26-27 0.0 40.125 0.0 0.0 0.0 28-29 0.0 43.9 0.0 0.0 0.0 30-31 0.0 56.9375 0.0 0.0 0.0 32-33 0.0 71.425 0.0 0.0 0.0 34-35 0.0 85.8625 0.0 0.0 0.0 36-37 0.0 93.9125 0.0 0.0 0.0 38-39 0.0 95.9 0.0 0.0 0.0 40-41 0.0 96.5875 0.0 0.0 0.0 42-43 0.0 97.2625 0.0 0.0 0.0 44-45 0.0 97.5125 0.0 0.0 0.0 46-47 0.0 97.675 0.0 0.0 0.0 48-49 0.0 97.725 0.0 0.0 0.0 50-51 0.0 97.725 0.0 0.0 0.0 52-53 0.0 97.725 0.0 0.0 0.0 54-55 0.0 97.725 0.0 0.0 0.0 56-57 0.0 97.725 0.0 0.0 0.0 58-59 0.0 97.725 0.0 0.0 0.0 60-61 0.0 97.725 0.0 0.0 0.0 62-63 0.0 97.725 0.0 0.0 0.0 64-65 0.0 97.725 0.0 0.0 0.0 66-67 0.0 97.725 0.0 0.0 0.0 68-69 0.0 97.725 0.0 0.0 0.0 70-71 0.0 97.725 0.0 0.0 0.0 72-73 0.0 97.725 0.0 0.0 0.0 74-75 0.0 97.725 0.0 0.0 0.0 76-77 0.0 97.725 0.0 0.0 0.0 78-79 0.0 97.725 0.0 0.0 0.0 80-81 0.0 97.7375 0.0 0.0 0.0 82-83 0.0 97.75 0.0 0.0 0.0 84-85 0.0 97.7625 0.0 0.0 0.0 86-87 0.0 97.775 0.0 0.0 0.0 88-89 0.0 97.775 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGTA 20 1.5392321E-5 95.00001 4 GATGTAG 20 1.5392321E-5 95.00001 5 TAGCCAA 20 1.5392321E-5 95.00001 9 GGATTGT 40 5.456968E-12 95.00001 2 CGGATGT 20 1.5392321E-5 95.00001 3 GATTGTA 40 5.456968E-12 95.00001 3 ATTGTAG 40 5.456968E-12 95.00001 4 TGTAGCC 20 1.5392321E-5 95.00001 7 ATGTAGC 20 1.5392321E-5 95.00001 6 GTAGCCA 20 1.5392321E-5 95.00001 8 GGCGGAT 20 1.5392321E-5 95.00001 1 GTAGACC 60 0.0 95.0 7 TTGTAGT 45 0.0 95.0 5 AGTAGAC 60 0.0 95.0 6 TAGTTCA 50 0.0 95.0 8 GAGTAGA 60 0.0 95.0 5 CGAGTAG 60 0.0 95.0 4 AGACCTT 60 0.0 95.0 9 ATCGAGT 60 0.0 95.0 2 TCGAGTA 60 0.0 95.0 3 >>END_MODULE Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261630 READS because READLEN < 1 Read 261630 spots for SRR6941583.sra Written 261630 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra Rejected 261618 READS because READLEN < 1 Read 261618 spots for SRR6941583.sra Written 261618 spots for SRR6941583.sra SRR ids: ['SRR6941583.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vhwh7mkf SRR6941583.sra spots: 5232372 blocks: [[1, 261618], [261619, 523236], [523237, 784854], [784855, 1046472], [1046473, 1308090], [1308091, 1569708], [1569709, 1831326], [1831327, 2092944], [2092945, 2354562], [2354563, 2616180], [2616181, 2877798], [2877799, 3139416], [3139417, 3401034], [3401035, 3662652], [3662653, 3924270], [3924271, 4185888], [4185889, 4447506], [4447507, 4709124], [4709125, 4970742], [4970743, 5232372]] SRR6941583 file size 1249716 SRR6941583 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 SRR6941583 SRR6941583_1.fastq Input file: SRR6941583_1.fastq trimmed: SRR6941583-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 Fri Dec 6 12:08:45 2024 >> started Fri Dec 6 12:08:49 2024 >> done (3.737s) 5232372 reads processed; of these: 63 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 5232302 (100.00%) reads available; of these: 619638 (11.84%) trimmed reads available after processing 4612664 (88.16%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 7 0.00% 20 6 0.00% 21 9 0.00% 22 11 0.00% 23 8 0.00% 24 14 0.00% 25 17 0.00% 26 16 0.00% 27 22 0.00% 28 18 0.00% 29 50 0.00% 30 43 0.00% 31 45 0.00% 32 68 0.00% 33 35 0.00% 34 71 0.00% 35 48 0.00% 36 43 0.00% 37 44 0.00% 38 43 0.00% 39 55 0.00% 40 74 0.00% 41 65 0.00% 42 68 0.00% 43 73 0.00% 44 48 0.00% 45 95 0.00% 46 95 0.00% 47 89 0.00% 48 64 0.00% 49 68 0.00% 50 40 0.00% 51 72 0.00% 52 40 0.00% 53 59 0.00% 54 67 0.00% 55 70 0.00% 56 76 0.00% 57 97 0.00% 58 100 0.00% 59 109 0.00% 60 128 0.00% 61 136 0.00% 62 128 0.00% 63 110 0.00% 64 124 0.00% 65 116 0.00% 66 156 0.00% 67 210 0.00% 68 270 0.01% 69 278 0.01% 70 358 0.01% 71 354 0.01% 72 519 0.01% 73 855 0.02% 74 2490 0.05% 75 1825 0.03% 76 884 0.02% 77 415 0.01% 78 493 0.01% 79 460 0.01% 80 497 0.01% 81 481 0.01% 82 603 0.01% 83 714 0.01% 84 1173 0.02% 85 1637 0.03% 86 1931 0.04% 87 2263 0.04% 88 2529 0.05% 89 3444 0.07% 90 3995 0.08% 91 6045 0.12% 92 8489 0.16% 93 14395 0.28% 94 25092 0.48% 95 54869 1.05% 96 60387 1.15% 97 73968 1.41% 98 91647 1.75% 99 151502 2.90% 100 101516 1.94% 101 4612664 88.16% 5232302 reads passed initial QC criterion=sequence-density sequence-density=97.65 sequence-density-rank=1 fanout-score=21.75 fanout-score-rank=1 prefix-density=97.94 prefix-fanout=21.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=97.65 sequence-density-rank=1 fanout-score=21.75 fanout-score-rank=1 prefix-density=97.94 prefix-fanout=21.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR6941583 - Input file: STDIN trimmed: SRR6941583-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGA -- 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 Fri Dec 6 12:09:05 2024 >> started Fri Dec 6 12:09:11 2024 >> done (5.823s) 5125520 reads processed; of these: 56536 ( 1.10%) short reads filtered out after trimming by size control 16740 ( 0.33%) empty reads filtered out after trimming by size control 5052244 (98.57%) reads available; of these: 5021306 (99.39%) trimmed reads available after processing 30938 ( 0.61%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 19829 0.39% 19 45972 0.91% 20 58707 1.16% 21 286905 5.68% 22 263171 5.21% 23 148587 2.94% 24 1003025 19.85% 25 136926 2.71% 26 117033 2.32% 27 94129 1.86% 28 102677 2.03% 29 324856 6.43% 30 538584 10.66% 31 325730 6.45% 32 372537 7.37% 33 430845 8.53% 34 275395 5.45% 35 252519 5.00% 36 84939 1.68% 37 41030 0.81% 38 20231 0.40% 39 13357 0.26% 40 18352 0.36% 41 18030 0.36% 42 14014 0.28% 43 3326 0.07% 44 3605 0.07% 45 3316 0.07% 46 977 0.02% 47 1432 0.03% 48 505 0.01% 49 205 0.00% 50 98 0.00% 51 81 0.00% 52 33 0.00% 53 51 0.00% 54 45 0.00% 55 29 0.00% 56 32 0.00% 57 31 0.00% 58 29 0.00% 59 32 0.00% 60 26 0.00% 61 28 0.00% 62 27 0.00% 63 17 0.00% 64 19 0.00% 65 19 0.00% 66 34 0.00% 67 38 0.00% 68 45 0.00% 69 56 0.00% 70 57 0.00% 71 44 0.00% 72 50 0.00% 73 44 0.00% 74 48 0.00% 75 54 0.00% 76 62 0.00% 77 147 0.00% 78 54 0.00% 79 60 0.00% 80 210 0.00% 81 102 0.00% 82 124 0.00% 83 119 0.00% 84 60 0.00% 85 65 0.00% 86 75 0.00% 87 104 0.00% 88 65 0.00% 89 83 0.00% 90 97 0.00% 91 142 0.00% 92 157 0.00% 93 208 0.00% 94 270 0.01% 95 316 0.01% 96 292 0.01% 97 393 0.01% 98 765 0.02% 99 736 0.01% 100 727 0.01% 101 24998 0.49% criterion=sequence-density sequence-density=13.88 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.33 sequence-density-rank=14 fanout-score=41.72 fanout-score-rank=1 prefix-density=13.55 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAA Started job on | Dec 06 12:09:29 Started mapping on | Dec 06 12:09:29 Finished on | Dec 06 12:09:47 Mapping speed, Million of reads per hour | 1031.81 Number of input reads | 5159026 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 848451 Uniquely mapped reads % | 16.45% Average mapped length | 25.03 Number of splices: Total | 21594 Number of splices: Annotated (sjdb) | 1936 Number of splices: GT/AG | 20847 Number of splices: GC/AG | 657 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 87 Mismatch rate per base, % | 1.07% Deletion rate per base | 0.01% Deletion average length | 1.28 Insertion rate per base | 0.00% Insertion average length | 1.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3442788 % of reads mapped to multiple loci | 66.73% Number of reads mapped to too many loci | 618311 % of reads mapped to too many loci | 11.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.05% % of reads unmapped: other | 0.79% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 867787 867787 867787 N_multimapping 3442788 3442788 3442788 N_noFeature 577768 676908 745018 N_ambiguous 8764 3952 611 UnstrandedReadsAssigned:261919 PositiveStrandReadsAssigned:167591 NegativeStrandReadsAssigned:102822 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR6941583 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: SRR6941583-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,159,026 reads, 2,226,141 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 942 rounds 52973 SRR6941583.ke.tsv 35125 SRR6941583.se.tsv 88098 total ==> SRR6941583.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 0 0 PNS24243 293 194 2 1.97945 KQK14069 1603 1504 6.49906 0.829695 KQK14071 474 375 0 0 ==> SRR6941583.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 3 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 2 BRADI_1g74790v3 10 BRADI_1g09890v3 14 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR6941583 completed mapping pipeline successfully