Starting /dee2/code/volunteer_pipeline.sh SRR6941540 current disk space = 1551512563712 free memory = 1333901908 SRR6941540 SRAfilesize 4f3df7357ec9958beff4ab0b64c5a758 SRR6941540.sra SRR6941540.sra file validated SRR6941540 is single end SRR6941540 is conventional basespace SRR6941540 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941540_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.21375 34.0 33.0 34.0 32.0 34.0 2 33.2835 34.0 33.0 34.0 32.0 34.0 3 33.00775 34.0 33.0 34.0 31.0 34.0 4 33.17 34.0 33.0 34.0 32.0 34.0 5 33.197 34.0 33.0 34.0 33.0 34.0 6 36.9055 38.0 37.0 38.0 36.0 38.0 7 37.3325 38.0 38.0 38.0 36.0 38.0 8 37.5395 38.0 38.0 38.0 37.0 38.0 9 37.584 38.0 38.0 38.0 38.0 38.0 10-11 37.470125 38.0 38.0 38.0 37.5 38.0 12-13 37.413 38.0 38.0 38.0 37.0 38.0 14-15 37.4285 38.0 38.0 38.0 37.0 38.0 16-17 36.087125 38.0 37.0 38.0 31.0 38.0 18-19 36.8335 38.0 37.5 38.0 33.5 38.0 20-21 36.072874999999996 38.0 38.0 38.0 30.0 38.0 22-23 37.15675 38.0 38.0 38.0 36.5 38.0 24-25 37.401125 38.0 38.0 38.0 37.0 38.0 26-27 37.378 38.0 38.0 38.0 37.0 38.0 28-29 37.455124999999995 38.0 38.0 38.0 37.5 38.0 30-31 37.330625 38.0 38.0 38.0 37.0 38.0 32-33 37.268625 38.0 38.0 38.0 37.0 38.0 34-35 37.22525 38.0 38.0 38.0 37.0 38.0 36-37 37.207750000000004 38.0 38.0 38.0 36.5 38.0 38-39 37.19325 38.0 38.0 38.0 36.5 38.0 40-41 37.042625 38.0 38.0 38.0 36.5 38.0 42-43 36.947375 38.0 38.0 38.0 36.0 38.0 44-45 36.945375 38.0 38.0 38.0 35.5 38.0 46-47 36.834875 38.0 38.0 38.0 35.5 38.0 48-49 36.957375 38.0 38.0 38.0 35.5 38.0 50-51 36.80375 38.0 38.0 38.0 36.0 38.0 52-53 36.947125 38.0 38.0 38.0 36.0 38.0 54-55 37.1155 38.0 38.0 38.0 36.5 38.0 56-57 37.045375 38.0 38.0 38.0 36.5 38.0 58-59 37.211749999999995 38.0 38.0 38.0 37.0 38.0 60-61 37.254875 38.0 38.0 38.0 37.0 38.0 62-63 37.011624999999995 38.0 38.0 38.0 36.0 38.0 64-65 36.723749999999995 38.0 38.0 38.0 34.5 38.0 66-67 36.587374999999994 38.0 38.0 38.0 34.0 38.0 68-69 36.870999999999995 38.0 38.0 38.0 35.0 38.0 70-71 36.4525 38.0 38.0 38.0 33.5 38.0 72-73 35.97475 38.0 37.0 38.0 30.5 38.0 74-75 35.377375 38.0 36.0 38.0 28.0 38.0 76-77 35.668499999999995 38.0 37.0 38.0 29.5 38.0 78-79 36.208875 38.0 37.5 38.0 33.5 38.0 80-81 36.548625 38.0 38.0 38.0 34.5 38.0 82-83 36.470875 38.0 38.0 38.0 35.0 38.0 84-85 36.554 38.0 38.0 38.0 35.0 38.0 86-87 36.414375 38.0 38.0 38.0 35.0 38.0 88-89 36.45025 38.0 38.0 38.0 34.0 38.0 90-91 36.3935 38.0 38.0 38.0 34.5 38.0 92-93 36.359625 38.0 38.0 38.0 34.5 38.0 94-95 35.972624999999994 38.0 38.0 38.0 34.0 38.0 96-97 34.619375 38.0 36.5 38.0 27.5 38.0 98-99 32.780125 38.0 35.0 38.0 8.5 38.0 100-101 30.8285 38.0 32.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 1.0 15 2.0 16 0.0 17 0.0 18 2.0 19 0.0 20 0.0 21 1.0 22 2.0 23 2.0 24 2.0 25 10.0 26 17.0 27 26.0 28 26.0 29 22.0 30 27.0 31 46.0 32 66.0 33 112.0 34 165.0 35 374.0 36 710.0 37 2385.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.725 20.075000000000003 12.7 24.5 2 35.426569927445584 31.573680260195147 15.88691518638979 17.112834625969477 3 34.675 16.75 27.125 21.45 4 26.200000000000003 34.325 12.975 26.5 5 44.3 15.975 26.05 13.675 6 19.650000000000002 35.5 27.275 17.575 7 49.725 19.425 20.474999999999998 10.375 8 20.849999999999998 12.6 52.025 14.524999999999999 9 15.9 49.65 20.4 14.05 10-11 41.0875 24.962500000000002 19.975 13.975000000000001 12-13 15.187500000000002 12.375 26.875 45.5625 14-15 18.462500000000002 42.262499999999996 27.224999999999998 12.049999999999999 16-17 28.075 14.9875 45.300000000000004 11.637500000000001 18-19 44.9125 20.125 24.212500000000002 10.75 20-21 12.0625 25.8625 40.6625 21.4125 22-23 32.0375 31.412499999999998 21.775 14.774999999999999 24-25 33.2625 32.35 17.95 16.4375 26-27 33.9125 26.8125 19.037499999999998 20.2375 28-29 17.712500000000002 32.800000000000004 21.6875 27.800000000000004 30-31 23.825 10.9875 39.0125 26.174999999999997 32-33 27.3625 14.399999999999999 29.599999999999998 28.6375 34-35 34.9125 21.875 30.049999999999997 13.1625 36-37 38.587500000000006 23.8375 27.474999999999998 10.100000000000001 38-39 22.075 24.025 35.55 18.35 40-41 19.9375 14.35 31.724999999999998 33.9875 42-43 33.9125 17.5625 23.974999999999998 24.55 44-45 53.6375 11.4 16.925 18.0375 46-47 37.4125 21.1125 18.087500000000002 23.3875 48-49 25.837500000000002 22.1875 18.1125 33.862500000000004 50-51 27.150000000000002 27.950000000000003 7.875 37.025000000000006 52-53 31.587500000000002 43.3 6.15 18.9625 54-55 25.687500000000004 31.474999999999998 16.275000000000002 26.5625 56-57 13.7875 31.4875 14.224999999999998 40.5 58-59 18.587500000000002 20.4 21.912499999999998 39.1 60-61 15.174999999999999 20.349999999999998 16.9125 47.5625 62-63 23.65 21.837500000000002 17.962500000000002 36.55 64-65 16.675 23.150000000000002 25.874999999999996 34.300000000000004 66-67 19.275000000000002 12.35 22.5 45.875 68-69 24.637500000000003 10.8625 19.875 44.625 70-71 19.975 17.6375 24.9125 37.475 72-73 19.037499999999998 15.950000000000001 26.9125 38.1 74-75 15.512500000000001 11.4625 29.375 43.65 76-77 18.75 10.7375 40.75 29.762499999999996 78-79 22.0875 10.35 39.5 28.0625 80-81 20.962500000000002 13.2875 34.849999999999994 30.9 82-83 28.15 7.1 34.175 30.575000000000003 84-85 22.35 4.5375 34.862500000000004 38.25 86-87 18.8875 9.0 42.9875 29.125 88-89 12.987499999999999 22.3125 41.9875 22.7125 90-91 12.662499999999998 25.15 37.8125 24.375 92-93 20.150000000000002 30.337500000000002 30.112499999999997 19.400000000000002 94-95 14.6 46.0625 27.875 11.4625 96-97 12.812499999999998 65.525 17.175 4.4875 98-99 6.3375 83.75 6.325 3.5875 100-101 2.675 89.8375 3.9375 3.55 >>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 0.0 33 0.0 34 0.5 35 1.5 36 1.5 37 1.5 38 2.5 39 5.5 40 7.5 41 8.5 42 10.0 43 16.0 44 63.0 45 141.5 46 379.0 47 532.5 48 380.0 49 323.5 50 299.5 51 202.0 52 276.5 53 404.0 54 385.5 55 242.0 56 110.0 57 80.5 58 60.0 59 26.0 60 21.0 61 13.0 62 3.0 63 1.5 64 0.5 65 0.5 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 pass #Base N-Count 1 0.0 2 0.075 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 fail #Total Deduplicated Percentage 43.15 #Duplication Level Percentage of deduplicated Percentage of total 1 84.58864426419467 36.5 2 6.199304750869061 5.35 3 2.4913093858632678 3.225 4 1.4484356894553883 2.5 5 0.5793742757821553 1.25 6 0.5793742757821553 1.5 7 0.4634994206257242 1.4000000000000001 8 0.28968713789107764 1.0 9 0.28968713789107764 1.125 >10 2.4913093858632678 22.7 >50 0.4055619930475087 12.45 >100 0.17381228273464658 11.0 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 204 5.1 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 120 3.0 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 116 2.9000000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 80 2.0 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 76 1.9 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 76 1.9 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 76 1.9 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 72 1.7999999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 59 1.4749999999999999 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 59 1.4749999999999999 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 50 1.25 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 47 1.175 Illumina Small RNA Adapter 2 (100% over 21bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 41 1.0250000000000001 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 40 1.0 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 37 0.9249999999999999 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 35 0.8750000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 34 0.8500000000000001 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 26bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 31 0.775 RNA PCR Primer, Index 1 (100% over 29bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 27 0.675 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 27 0.675 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 27 0.675 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 24 0.6 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 23 0.575 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 23 0.575 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 23 0.575 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGC 22 0.5499999999999999 RNA PCR Primer, Index 18 (100% over 50bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 22 0.5499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 21 0.525 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 20 0.5 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 18 0.44999999999999996 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 22bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 17 0.42500000000000004 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 16 0.4 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 15 0.375 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 15 0.375 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 13 0.325 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 12 0.3 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 12 0.3 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 12 0.3 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 10 0.25 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 10 0.25 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 8 0.2 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 8 0.2 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 8 0.2 No Hit GGCGGATGTAGCCAAGAGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 7 0.17500000000000002 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGG 6 0.15 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 6 0.15 No Hit GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 6 0.15 No Hit CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 5 0.125 No Hit TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCG 5 0.125 No Hit CATCGAGTAGACCTTGTTACTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 5 0.125 No Hit GGGATTGTAGTTCAATGGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 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 0.65 0.0 0.0 0.0 2 0.0 0.65 0.0 0.0 0.0 3 0.0 0.65 0.0 0.0 0.0 4 0.0 0.675 0.0 0.0 0.0 5 0.0 0.7 0.0 0.0 0.0 6 0.0 0.7 0.0 0.0 0.0 7 0.0 0.7 0.0 0.0 0.0 8 0.0 0.725 0.0 0.0 0.0 9 0.0 0.725 0.0 0.0 0.0 10-11 0.0 0.7375 0.0 0.0 0.0 12-13 0.0 0.7625 0.0 0.0 0.0 14-15 0.0 0.775 0.0 0.0 0.0 16-17 0.0 0.8125 0.0 0.0 0.0 18-19 0.0 1.025 0.0 0.0 0.0 20-21 0.0 1.525 0.0 0.0 0.0 22-23 0.0 5.625 0.0 0.0 0.0 24-25 0.0 14.3 0.0 0.0 0.0 26-27 0.0 22.85 0.0 0.0 0.0 28-29 0.0 26.3375 0.0 0.0 0.0 30-31 0.0 37.0125 0.0 0.0 0.0 32-33 0.0 53.9 0.0 0.0 0.0 34-35 0.0 75.42500000000001 0.0 0.0 0.0 36-37 0.0 88.5 0.0 0.0 0.0 38-39 0.0 91.94999999999999 0.0 0.0 0.0 40-41 0.0 93.5625 0.0 0.0 0.0 42-43 0.0 96.025 0.0 0.0 0.0 44-45 0.0 96.95 0.0 0.0 0.0 46-47 0.0 97.3375 0.0 0.0 0.0 48-49 0.0 97.5125 0.0 0.0 0.0 50-51 0.0 97.525 0.0 0.0 0.0 52-53 0.0 97.55 0.0 0.0 0.0 54-55 0.0 97.55 0.0 0.0 0.0 56-57 0.0 97.55 0.0 0.0 0.0 58-59 0.0 97.55 0.0 0.0 0.0 60-61 0.0 97.55 0.0 0.0 0.0 62-63 0.0 97.55 0.0 0.0 0.0 64-65 0.0 97.55 0.0 0.0 0.0 66-67 0.0 97.55 0.0 0.0 0.0 68-69 0.0 97.55 0.0 0.0 0.0 70-71 0.0 97.55 0.0 0.0 0.0 72-73 0.0 97.55 0.0 0.0 0.0 74-75 0.0 97.55 0.0 0.0 0.0 76-77 0.0 97.55 0.0 0.0 0.0 78-79 0.0 97.55 0.0 0.0 0.0 80-81 0.0 97.55 0.0 0.0 0.0 82-83 0.0 97.55 0.0 0.0 0.0 84-85 0.0 97.55 0.0 0.0 0.0 86-87 0.0 97.55 0.0 0.0 0.0 88-89 0.0 97.55 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 20 1.5392321E-5 95.00001 9 TAGCTCA 20 1.5392321E-5 95.00001 8 GGATGTA 25 3.8289727E-7 95.0 4 GAGCGTA 15 6.142176E-4 95.0 3 TTGTATC 15 6.142176E-4 95.0 4 TTGTAGT 60 0.0 95.0 5 AGGATAG 15 6.142176E-4 95.0 4 TCAGGAT 15 6.142176E-4 95.0 2 TATCGCG 15 6.142176E-4 95.0 7 GATGTAG 25 3.8289727E-7 95.0 5 TCGCGCG 15 6.142176E-4 95.0 9 TAGCCAA 25 3.8289727E-7 95.0 9 GTATCGC 15 6.142176E-4 95.0 6 CGTAGTT 15 6.142176E-4 95.0 6 CGGATGT 25 3.8289727E-7 95.0 3 GCGGATG 25 3.8289727E-7 95.0 2 GATTGTA 60 0.0 95.0 3 TAGTTCA 75 0.0 95.0 8 GGATAGC 15 6.142176E-4 95.0 5 ATAGCTC 15 6.142176E-4 95.0 7 >>END_MODULE Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283921 READS because READLEN < 1 Read 283921 spots for SRR6941540.sra Written 283921 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra Rejected 283902 READS because READLEN < 1 Read 283902 spots for SRR6941540.sra Written 283902 spots for SRR6941540.sra SRR ids: ['SRR6941540.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_onz3ct28 SRR6941540.sra spots: 5678059 blocks: [[1, 283902], [283903, 567804], [567805, 851706], [851707, 1135608], [1135609, 1419510], [1419511, 1703412], [1703413, 1987314], [1987315, 2271216], [2271217, 2555118], [2555119, 2839020], [2839021, 3122922], [3122923, 3406824], [3406825, 3690726], [3690727, 3974628], [3974629, 4258530], [4258531, 4542432], [4542433, 4826334], [4826335, 5110236], [5110237, 5394138], [5394139, 5678059]] SRR6941540 file size 1356350 SRR6941540 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 SRR6941540 SRR6941540_1.fastq Input file: SRR6941540_1.fastq trimmed: SRR6941540-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 10:45:00 2024 >> started Fri Dec 6 10:45:03 2024 >> done (2.961s) 5678059 reads processed; of these: 102 ( 0.00%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 5677941 (100.00%) reads available; of these: 685719 (12.08%) trimmed reads available after processing 4992222 (87.92%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 9 0.00% 20 14 0.00% 21 5 0.00% 22 12 0.00% 23 15 0.00% 24 19 0.00% 25 22 0.00% 26 21 0.00% 27 29 0.00% 28 38 0.00% 29 79 0.00% 30 103 0.00% 31 58 0.00% 32 86 0.00% 33 91 0.00% 34 117 0.00% 35 142 0.00% 36 178 0.00% 37 192 0.00% 38 180 0.00% 39 185 0.00% 40 205 0.00% 41 146 0.00% 42 147 0.00% 43 149 0.00% 44 128 0.00% 45 189 0.00% 46 190 0.00% 47 139 0.00% 48 111 0.00% 49 89 0.00% 50 112 0.00% 51 109 0.00% 52 114 0.00% 53 143 0.00% 54 124 0.00% 55 138 0.00% 56 202 0.00% 57 135 0.00% 58 127 0.00% 59 203 0.00% 60 261 0.00% 61 202 0.00% 62 186 0.00% 63 155 0.00% 64 163 0.00% 65 180 0.00% 66 240 0.00% 67 270 0.00% 68 410 0.01% 69 490 0.01% 70 715 0.01% 71 650 0.01% 72 881 0.02% 73 2056 0.04% 74 11562 0.20% 75 6360 0.11% 76 2110 0.04% 77 761 0.01% 78 834 0.01% 79 737 0.01% 80 790 0.01% 81 789 0.01% 82 915 0.02% 83 1103 0.02% 84 1793 0.03% 85 1713 0.03% 86 1808 0.03% 87 1874 0.03% 88 2025 0.04% 89 2916 0.05% 90 4005 0.07% 91 5613 0.10% 92 7660 0.13% 93 14620 0.26% 94 26078 0.46% 95 66129 1.16% 96 69285 1.22% 97 76236 1.34% 98 147214 2.59% 99 149699 2.64% 100 69728 1.23% 101 4992222 87.92% 5677941 reads passed initial QC criterion=sequence-density sequence-density=97.48 sequence-density-rank=1 fanout-score=24.63 fanout-score-rank=1 prefix-density=97.41 prefix-fanout=24.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=97.48 sequence-density-rank=1 fanout-score=24.63 fanout-score-rank=1 prefix-density=97.41 prefix-fanout=24.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941540 - Input file: STDIN trimmed: SRR6941540-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:45:17 2024 >> started Fri Dec 6 10:45:25 2024 >> done (7.369s) 5562065 reads processed; of these: 14259 ( 0.26%) short reads filtered out after trimming by size control 38187 ( 0.69%) empty reads filtered out after trimming by size control 5509619 (99.06%) reads available; of these: 5476828 (99.40%) trimmed reads available after processing 32791 ( 0.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6019 0.11% 19 15888 0.29% 20 24021 0.44% 21 148492 2.70% 22 131470 2.39% 23 92847 1.69% 24 639412 11.61% 25 110045 2.00% 26 105000 1.91% 27 86328 1.57% 28 96891 1.76% 29 306553 5.56% 30 572739 10.40% 31 427608 7.76% 32 536293 9.73% 33 662014 12.02% 34 475366 8.63% 35 417812 7.58% 36 174690 3.17% 37 95781 1.74% 38 53575 0.97% 39 42018 0.76% 40 75698 1.37% 41 77253 1.40% 42 54692 0.99% 43 13637 0.25% 44 15278 0.28% 45 10334 0.19% 46 3503 0.06% 47 3506 0.06% 48 1369 0.02% 49 701 0.01% 50 412 0.01% 51 360 0.01% 52 202 0.00% 53 159 0.00% 54 108 0.00% 55 100 0.00% 56 99 0.00% 57 57 0.00% 58 45 0.00% 59 62 0.00% 60 107 0.00% 61 57 0.00% 62 38 0.00% 63 35 0.00% 64 31 0.00% 65 39 0.00% 66 43 0.00% 67 45 0.00% 68 69 0.00% 69 57 0.00% 70 88 0.00% 71 68 0.00% 72 77 0.00% 73 61 0.00% 74 71 0.00% 75 77 0.00% 76 81 0.00% 77 170 0.00% 78 66 0.00% 79 74 0.00% 80 195 0.00% 81 76 0.00% 82 91 0.00% 83 97 0.00% 84 71 0.00% 85 46 0.00% 86 67 0.00% 87 103 0.00% 88 84 0.00% 89 79 0.00% 90 115 0.00% 91 160 0.00% 92 167 0.00% 93 216 0.00% 94 273 0.00% 95 269 0.00% 96 295 0.01% 97 365 0.01% 98 606 0.01% 99 424 0.01% 100 439 0.01% 101 25590 0.46% criterion=sequence-density sequence-density=16.69 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.40 sequence-density-rank=14 fanout-score=40.91 fanout-score-rank=1 prefix-density=16.41 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAAA Started job on | Dec 06 10:45:44 Started mapping on | Dec 06 10:45:45 Finished on | Dec 06 10:46:04 Mapping speed, Million of reads per hour | 1065.88 Number of input reads | 5625495 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 694475 Uniquely mapped reads % | 12.35% Average mapped length | 27.42 Number of splices: Total | 15384 Number of splices: Annotated (sjdb) | 2186 Number of splices: GT/AG | 14764 Number of splices: GC/AG | 501 Number of splices: AT/AC | 5 Number of splices: Non-canonical | 114 Mismatch rate per base, % | 0.86% Deletion rate per base | 0.01% Deletion average length | 1.35 Insertion rate per base | 0.00% Insertion average length | 1.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4013577 % of reads mapped to multiple loci | 71.35% Number of reads mapped to too many loci | 676536 % of reads mapped to too many loci | 12.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.80% % of reads unmapped: other | 0.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 917443 917443 917443 N_multimapping 4013577 4013577 4013577 N_noFeature 409303 553542 546585 N_ambiguous 8416 4451 382 UnstrandedReadsAssigned:276756 PositiveStrandReadsAssigned:136482 NegativeStrandReadsAssigned:147508 Dataset is classified unstranded MeadianReadLen=31 20thPercentileLength=25 echo kmer=21 SRR6941540 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: SRR6941540-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,625,495 reads, 2,750,284 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 898 rounds 52973 SRR6941540.ke.tsv 35125 SRR6941540.se.tsv 88098 total ==> SRR6941540.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 3 2.3177 KQK14069 1603 1504 6.68478 0.666157 KQK14071 474 375 0 0 ==> SRR6941540.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 6 BRADI_1g09890v3 12 BRADI_1g77505v3 2 BRADI_1g48960v3 0 SRR6941540 completed mapping pipeline successfully