Starting /dee2/code/volunteer_pipeline.sh SRR10225135 current disk space = 3052491669504 free memory = 1411891156 SRR10225135 SRAfilesize acf786d51d9511288ff15484084c3542 SRR10225135.sra SRR10225135.sra file validated SRR10225135 is paired end SRR10225135 is conventional basespace SRR10225135 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225135_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.905 34.0 33.0 34.0 31.0 34.0 2 33.10275 34.0 33.0 34.0 31.0 34.0 3 33.1445 34.0 33.0 34.0 31.0 34.0 4 36.469 37.0 37.0 37.0 35.0 37.0 5 36.424 37.0 37.0 37.0 35.0 37.0 6 36.3585 37.0 37.0 37.0 35.0 37.0 7 36.428 37.0 37.0 37.0 35.0 37.0 8 36.42375 37.0 37.0 37.0 35.0 37.0 9 38.29725 39.0 39.0 39.0 37.0 39.0 10-11 38.23025 39.0 39.0 39.0 37.0 39.0 12-13 38.223749999999995 39.0 39.0 39.0 37.0 39.0 14-15 39.8345 41.0 40.0 41.0 38.0 41.0 16-17 39.7675 41.0 40.0 41.0 37.5 41.0 18-19 39.724875 41.0 40.0 41.0 37.0 41.0 20-21 39.677375 41.0 40.0 41.0 37.0 41.0 22-23 39.668000000000006 41.0 40.0 41.0 37.0 41.0 24-25 39.610749999999996 41.0 40.0 41.0 37.0 41.0 26-27 39.483625 41.0 40.0 41.0 37.0 41.0 28-29 39.322 41.0 39.0 41.0 36.0 41.0 30-31 39.273125 41.0 39.0 41.0 36.0 41.0 32-33 39.085375 41.0 39.0 41.0 36.0 41.0 34-35 38.977999999999994 40.5 39.0 41.0 35.5 41.0 36-37 38.789625 40.0 38.5 41.0 35.0 41.0 38-39 38.801 40.0 38.0 41.0 35.0 41.0 40-41 38.681 40.0 38.0 41.0 35.0 41.0 42-43 38.4035 40.0 38.0 41.0 34.5 41.0 44-45 38.68075 40.0 39.0 41.0 35.0 41.0 46-47 38.69175 41.0 38.5 41.0 34.5 41.0 48-49 38.636375 41.0 38.0 41.0 35.0 41.0 50-51 38.549375 40.5 38.0 41.0 35.0 41.0 52-53 38.39975 40.0 38.0 41.0 34.0 41.0 54-55 38.164625 40.0 37.5 41.0 34.0 41.0 56-57 38.01375 40.0 37.0 41.0 33.5 41.0 58-59 37.698 40.0 37.0 41.0 33.0 41.0 60-61 37.53375 39.5 36.0 41.0 33.0 41.0 62-63 37.2455 39.0 35.5 41.0 33.0 41.0 64-65 36.915875 39.0 35.0 41.0 32.0 41.0 66-67 36.584125 37.5 35.0 40.0 32.0 41.0 68-69 36.18825 37.0 35.0 39.5 32.0 41.0 70-71 35.841875 36.5 35.0 39.0 32.0 41.0 72-73 35.405625 36.0 35.0 39.0 32.0 40.5 74-75 34.218125 35.5 35.0 37.5 29.5 39.0 76-77 33.813 35.0 35.0 37.0 30.0 39.0 78-79 33.508250000000004 35.0 35.0 36.5 29.5 38.5 80-81 33.163125 35.0 34.0 36.0 29.0 37.0 82-83 32.989125 35.0 34.0 36.0 29.5 37.0 84-85 32.832750000000004 35.0 34.0 35.5 29.0 36.5 86-87 32.53525 35.0 34.0 35.0 29.0 36.0 88-89 32.457375 35.0 34.0 35.0 29.0 36.0 90-91 32.317875 35.0 34.0 35.0 29.0 36.0 92-93 32.18125 35.0 34.0 35.0 29.0 35.5 94-95 32.0535 35.0 34.0 35.0 27.5 35.0 96-97 31.830875 35.0 34.0 35.0 26.5 35.0 98-99 31.782125 35.0 34.0 35.0 26.5 35.0 100 31.6935 35.0 34.0 35.0 26.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 0.0 9 3.0 10 3.0 11 4.0 12 2.0 13 5.0 14 4.0 15 3.0 16 3.0 17 6.0 18 5.0 19 6.0 20 5.0 21 9.0 22 9.0 23 5.0 24 14.0 25 19.0 26 21.0 27 26.0 28 50.0 29 91.0 30 40.0 31 53.0 32 71.0 33 87.0 34 120.0 35 192.0 36 350.0 37 854.0 38 1571.0 39 368.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.864593781344034 36.158475426278834 20.837512537612838 13.139418254764292 2 33.875 32.175 18.125 15.825 3 29.325000000000003 32.550000000000004 22.95 15.174999999999999 4 28.225 29.7 24.349999999999998 17.724999999999998 5 26.950000000000003 28.999999999999996 22.75 21.3 6 31.1 26.974999999999998 23.200000000000003 18.725 7 27.825 29.325000000000003 24.075 18.775 8 23.625 31.55 27.025 17.8 9 24.025 31.324999999999996 25.724999999999998 18.925 10-11 24.3875 31.05 25.887500000000003 18.675 12-13 24.462500000000002 28.3625 25.9625 21.212500000000002 14-15 23.625 29.475 26.325 20.575 16-17 22.5625 30.349999999999998 25.7875 21.3 18-19 24.7 27.474999999999998 26.987499999999997 20.837500000000002 20-21 22.7125 28.712500000000002 27.0625 21.512500000000003 22-23 24.349999999999998 30.15 25.887500000000003 19.6125 24-25 22.3 30.2875 25.775 21.637500000000003 26-27 23.799999999999997 28.512500000000003 26.9625 20.724999999999998 28-29 23.6625 29.65 25.4 21.2875 30-31 24.0 28.349999999999998 26.875 20.775 32-33 22.475 30.599999999999998 24.875 22.05 34-35 21.987499999999997 28.575 27.700000000000003 21.7375 36-37 24.45 28.9125 26.974999999999998 19.662499999999998 38-39 22.875 28.275 27.075 21.775 40-41 22.237499999999997 29.2 28.1375 20.424999999999997 42-43 23.2125 28.5875 26.6 21.6 44-45 22.125 28.1375 27.700000000000003 22.037499999999998 46-47 25.025 27.750000000000004 27.3625 19.8625 48-49 22.75 29.275000000000002 27.675 20.3 50-51 24.7 27.675 25.724999999999998 21.9 52-53 24.7 28.262500000000003 25.4375 21.6 54-55 23.2875 28.000000000000004 26.7625 21.95 56-57 22.7125 27.237499999999997 28.599999999999998 21.45 58-59 22.7 27.437499999999996 28.050000000000004 21.8125 60-61 24.0375 27.6 26.7625 21.6 62-63 22.275 28.025 29.562500000000004 20.1375 64-65 23.8875 29.275000000000002 26.75 20.0875 66-67 22.8375 30.575000000000003 26.7125 19.875 68-69 22.6 30.575000000000003 25.9875 20.837500000000002 70-71 22.31807951987997 30.545136284071017 26.269067266816705 20.86771692923231 72-73 23.65 30.325000000000003 26.137500000000003 19.8875 74-75 22.625 30.125 26.9625 20.2875 76-77 23.3 29.6875 26.424999999999997 20.5875 78-79 23.8625 29.5375 26.8 19.8 80-81 23.3875 28.975 27.462500000000002 20.175 82-83 23.9875 28.512500000000003 26.674999999999997 20.825 84-85 22.9375 28.95 27.5875 20.525 86-87 23.2875 28.799999999999997 27.950000000000003 19.9625 88-89 24.6125 28.712500000000002 26.474999999999998 20.200000000000003 90-91 23.4375 27.6125 27.187499999999996 21.762500000000003 92-93 22.787499999999998 28.95 27.175 21.087500000000002 94-95 23.3375 27.85 27.750000000000004 21.0625 96-97 23.7625 28.6375 27.2625 20.3375 98-99 23.0875 28.6375 27.425 20.849999999999998 100 23.549999999999997 26.75 29.575000000000003 20.125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 1.5 14 2.0 15 2.0 16 1.0 17 0.5 18 0.5 19 1.0 20 3.0 21 3.5 22 2.0 23 2.0 24 4.0 25 3.0 26 3.0 27 6.5 28 7.5 29 10.0 30 12.0 31 16.5 32 26.0 33 31.0 34 40.5 35 63.0 36 84.0 37 114.5 38 145.0 39 166.0 40 208.0 41 226.0 42 252.5 43 296.0 44 284.5 45 262.5 46 256.5 47 233.5 48 199.5 49 178.0 50 157.5 51 128.5 52 107.5 53 83.0 54 63.5 55 56.0 56 50.0 57 41.5 58 29.0 59 27.5 60 23.0 61 13.5 62 10.5 63 10.0 64 10.0 65 7.5 66 2.5 67 3.5 68 4.0 69 3.0 70 4.0 71 3.5 72 2.0 73 2.0 74 1.5 75 1.0 76 1.0 77 0.5 78 0.5 79 1.0 80 0.5 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 0.3 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 0.025 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.125 #Duplication Level Percentage of deduplicated Percentage of total 1 99.29778933680105 95.45 2 0.494148244473342 0.95 3 0.10403120936280884 0.3 4 0.02600780234070221 0.1 5 0.02600780234070221 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02600780234070221 0.375 >50 0.0 0.0 >100 0.02600780234070221 2.7 >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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATG 108 2.7 TruSeq Adapter, Index 10 (100% over 49bp) CAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTG 15 0.375 No Hit AATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGC 5 0.125 TruSeq Adapter, Index 10 (98% over 50bp) >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 3.125 0.0 0.0 0.0 0.0 2 3.125 0.0 0.0 0.0 0.0 3 3.125 0.0 0.0 0.0 0.0 4 3.125 0.0 0.0 0.0 0.0 5 3.125 0.0 0.0 0.0 0.0 6 3.125 0.0 0.0 0.0 0.0 7 3.125 0.0 0.0 0.0 0.0 8 3.125 0.0 0.0 0.0 0.0 9 3.125 0.0 0.0 0.0 0.0 10-11 3.15 0.0 0.0 0.0 0.0 12-13 3.225 0.0 0.0 0.0 0.0 14-15 3.225 0.0 0.0 0.0 0.0 16-17 3.225 0.0 0.0 0.0 0.0 18-19 3.225 0.0 0.0 0.0 0.0 20-21 3.225 0.0 0.0 0.0 0.0 22-23 3.225 0.0 0.0 0.0 0.0 24-25 3.225 0.0 0.0 0.0 0.0 26-27 3.225 0.0 0.0 0.0 0.0 28-29 3.225 0.0 0.0 0.0 0.0 30-31 3.225 0.0 0.0 0.0 0.0 32-33 3.225 0.0 0.0 0.0 0.0 34-35 3.275 0.0 0.0 0.0 0.0 36-37 3.3125 0.0 0.0 0.0 0.0 38-39 3.325 0.0 0.0 0.0 0.0 40-41 3.325 0.0 0.0 0.0 0.0 42-43 3.325 0.0 0.0 0.0 0.0 44-45 3.325 0.0 0.0 0.0 0.0 46-47 3.325 0.0 0.0 0.0 0.0 48-49 3.35 0.0 0.0 0.0 0.0 50-51 3.35 0.0 0.0 0.0 0.0 52-53 3.35 0.0 0.0 0.0 0.0 54-55 3.35 0.0 0.0 0.0 0.0 56-57 3.35 0.0 0.0 0.0 0.0 58-59 3.35 0.0 0.0 0.0 0.0 60-61 3.375 0.0 0.0 0.0 0.0 62-63 3.4 0.0 0.0 0.0 0.0 64-65 3.425 0.0 0.0 0.0 0.0 66-67 3.425 0.0 0.0 0.0 0.0 68-69 3.425 0.0 0.0 0.0 0.0 70-71 3.425 0.0 0.0 0.0 0.0 72-73 3.4375 0.0 0.0 0.0 0.0 74-75 3.45 0.0 0.0 0.0 0.0 76-77 3.45 0.0 0.0 0.0 0.0 78-79 3.475 0.0 0.0 0.0 0.0 80-81 3.5 0.0 0.0 0.0 0.0 82-83 3.5125 0.0 0.0 0.0 0.0 84-85 3.575 0.0 0.0 0.0 0.0 86-87 3.575 0.0 0.0 0.0 0.0 88 3.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR10225135 read2 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225135_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.19925 34.0 31.0 34.0 31.0 34.0 2 32.41025 34.0 31.0 34.0 31.0 34.0 3 32.4005 34.0 31.0 34.0 31.0 34.0 4 35.8715 37.0 37.0 37.0 35.0 37.0 5 35.7885 37.0 37.0 37.0 35.0 37.0 6 35.753 37.0 37.0 37.0 35.0 37.0 7 35.716 37.0 37.0 37.0 35.0 37.0 8 35.784 37.0 37.0 37.0 35.0 37.0 9 37.59475 39.0 39.0 39.0 35.0 39.0 10-11 37.572374999999994 39.0 39.0 39.0 35.0 39.0 12-13 37.540625000000006 39.0 39.0 39.0 35.0 39.0 14-15 39.02725 41.0 40.0 41.0 36.0 41.0 16-17 38.975 41.0 40.0 41.0 36.0 41.0 18-19 38.84125 41.0 39.5 41.0 35.5 41.0 20-21 38.842625 41.0 39.5 41.0 36.0 41.0 22-23 38.676625 41.0 39.0 41.0 35.0 41.0 24-25 38.572125 41.0 39.0 41.0 34.5 41.0 26-27 38.473875 41.0 39.0 41.0 34.5 41.0 28-29 38.337 41.0 39.0 41.0 34.0 41.0 30-31 38.06375 40.0 38.5 41.0 33.0 41.0 32-33 38.022000000000006 40.0 38.0 41.0 33.0 41.0 34-35 37.980875 40.0 38.0 41.0 33.0 41.0 36-37 37.888374999999996 40.0 38.0 41.0 33.0 41.0 38-39 37.829125 40.0 38.0 41.0 33.0 41.0 40-41 37.71875 40.0 38.0 41.0 33.0 41.0 42-43 37.631625 40.0 38.0 41.0 33.0 41.0 44-45 37.715625 40.0 38.0 41.0 33.0 41.0 46-47 37.859 40.5 38.0 41.0 33.0 41.0 48-49 37.7195 40.0 38.0 41.0 33.0 41.0 50-51 37.696625 40.0 38.0 41.0 33.0 41.0 52-53 37.50325 40.0 37.0 41.0 32.5 41.0 54-55 37.331125 40.0 37.0 41.0 32.0 41.0 56-57 37.111125 40.0 36.0 41.0 32.0 41.0 58-59 36.904375 40.0 36.0 41.0 31.5 41.0 60-61 36.708124999999995 39.0 36.0 41.0 31.5 41.0 62-63 36.444 39.0 35.0 41.0 31.5 41.0 64-65 35.936499999999995 38.5 35.0 41.0 31.0 41.0 66-67 35.235875 37.5 35.0 40.0 29.5 41.0 68-69 34.453 37.0 35.0 39.5 27.5 41.0 70-71 34.06325 36.5 35.0 39.0 26.5 41.0 72-73 33.582375 36.0 34.5 39.0 26.0 40.5 74-75 33.1695 35.5 34.0 37.5 25.0 39.5 76-77 32.857749999999996 35.0 34.0 37.0 25.0 39.0 78-79 32.4905 35.0 34.0 37.0 25.0 39.0 80-81 32.268375 35.0 34.0 36.0 25.0 37.5 82-83 31.932875 35.0 34.0 36.0 24.5 37.0 84-85 31.7105 35.0 34.0 35.5 24.0 37.0 86-87 31.467624999999998 35.0 33.5 35.0 23.0 36.0 88-89 31.35125 35.0 33.0 35.0 23.0 36.0 90-91 31.120874999999998 35.0 33.0 35.0 20.0 36.0 92-93 30.859875000000002 35.0 33.0 35.0 17.0 35.5 94-95 30.746000000000002 35.0 33.0 35.0 14.5 35.0 96-97 30.5955 35.0 33.0 35.0 4.5 35.0 98-99 30.417375 35.0 33.0 35.0 2.0 35.0 100 30.27225 35.0 33.0 35.0 2.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 34.0 3 9.0 4 3.0 5 8.0 6 1.0 7 10.0 8 7.0 9 5.0 10 4.0 11 4.0 12 1.0 13 10.0 14 9.0 15 7.0 16 6.0 17 11.0 18 10.0 19 12.0 20 10.0 21 15.0 22 13.0 23 18.0 24 36.0 25 71.0 26 40.0 27 29.0 28 26.0 29 41.0 30 40.0 31 54.0 32 55.0 33 106.0 34 132.0 35 187.0 36 295.0 37 772.0 38 1494.0 39 414.0 40 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.975 15.825 15.975 28.225 2 29.575000000000003 7.725 20.849999999999998 41.85 3 18.4 10.225 19.3 52.075 4 21.55 7.074999999999999 21.675 49.7 5 23.7 11.200000000000001 22.425 42.675000000000004 6 32.175 12.0 26.450000000000003 29.375 7 21.224999999999998 26.325 32.9 19.55 8 16.375 32.0 33.225 18.4 9 15.825 32.425 31.95 19.8 10-11 18.55 32.087500000000006 29.8875 19.475 12-13 18.987499999999997 28.15 30.85 22.0125 14-15 19.125 28.000000000000004 32.0625 20.8125 16-17 19.675 27.325 29.9375 23.0625 18-19 19.4875 29.15 30.5125 20.849999999999998 20-21 18.337500000000002 29.849999999999998 30.4625 21.349999999999998 22-23 21.75 28.549999999999997 27.950000000000003 21.75 24-25 19.7625 29.225 28.6625 22.35 26-27 18.1375 31.9875 27.962500000000002 21.912499999999998 28-29 20.724999999999998 29.7125 27.787499999999998 21.775 30-31 20.1125 29.525000000000002 28.549999999999997 21.8125 32-33 19.575 28.6375 29.562500000000004 22.225 34-35 20.525 29.625 27.575 22.275 36-37 18.712500000000002 30.075000000000003 28.962500000000002 22.25 38-39 19.525000000000002 27.5875 29.1875 23.7 40-41 21.05 28.299999999999997 27.3625 23.2875 42-43 21.275 28.462500000000002 28.499999999999996 21.762500000000003 44-45 20.849999999999998 29.812499999999996 27.325 22.0125 46-47 20.8875 28.299999999999997 27.425 23.3875 48-49 20.95 27.8875 27.212500000000002 23.95 50-51 20.962500000000002 28.0875 26.974999999999998 23.974999999999998 52-53 19.275000000000002 29.0875 28.599999999999998 23.0375 54-55 19.2375 28.3125 29.825000000000003 22.625 56-57 19.162499999999998 30.425 28.000000000000004 22.412499999999998 58-59 19.775000000000002 29.975 27.6875 22.5625 60-61 19.537499999999998 31.7375 26.3125 22.412499999999998 62-63 19.112499999999997 31.7625 26.650000000000002 22.475 64-65 20.6625 30.1375 27.1125 22.0875 66-67 19.025 31.2 27.125 22.650000000000002 68-69 19.787499999999998 31.0125 26.337500000000002 22.8625 70-71 19.525000000000002 30.375000000000004 27.3375 22.7625 72-73 20.1625 28.625 28.012500000000003 23.200000000000003 74-75 20.5875 29.562500000000004 27.0125 22.8375 76-77 20.962500000000002 28.8875 27.35 22.8 78-79 20.4 29.049999999999997 27.525 23.025000000000002 80-81 20.5 28.6125 27.737499999999997 23.150000000000002 82-83 20.4 28.7375 27.575 23.2875 84-85 20.5625 29.099999999999998 27.275 23.0625 86-87 19.7 28.849999999999998 27.450000000000003 24.0 88-89 20.1625 29.7875 27.187499999999996 22.8625 90-91 19.6 28.9 27.500000000000004 24.0 92-93 20.65 29.049999999999997 27.6 22.7 94-95 20.849999999999998 28.95 27.35 22.85 96-97 20.5625 28.599999999999998 27.6 23.2375 98-99 20.775 28.175 28.349999999999998 22.7 100 21.75 29.725 25.75 22.775000000000002 >>END_MODULE >>Per sequence GC content warn #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 0.5 8 1.0 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 1.0 16 1.0 17 1.5 18 3.5 19 4.0 20 4.5 21 4.5 22 4.0 23 5.5 24 6.0 25 9.0 26 10.0 27 13.0 28 16.5 29 15.5 30 24.5 31 40.0 32 44.0 33 54.5 34 70.0 35 81.5 36 111.0 37 133.0 38 150.5 39 180.0 40 202.5 41 212.5 42 217.5 43 215.0 44 241.0 45 249.5 46 216.0 47 197.5 48 186.5 49 167.5 50 141.0 51 115.5 52 95.0 53 80.5 54 63.0 55 55.5 56 56.0 57 52.0 58 46.5 59 41.0 60 31.5 61 25.5 62 21.5 63 16.5 64 14.0 65 11.5 66 7.0 67 4.5 68 5.0 69 4.0 70 2.5 71 2.5 72 4.0 73 4.0 74 2.0 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.625 #Duplication Level Percentage of deduplicated Percentage of total 1 98.58823529411764 94.27499999999999 2 1.0980392156862746 2.1 3 0.1830065359477124 0.525 4 0.052287581699346414 0.2 5 0.026143790849673207 0.125 6 0.026143790849673207 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.026143790849673207 2.625 >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 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 105 2.625 Illumina Single End PCR Primer 1 (100% over 50bp) GCACCCAAAACTACTAGAGAAGACCCAATAATAAAAAGACGAAACAAAGA 6 0.15 No Hit GACGCGTACACAAGACAAAGGATTTATAGGAACCCTTTGCTGTTTATTAT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 2.95 0.0 0.0 0.0 0.0 2 2.95 0.0 0.0 0.0 0.0 3 2.95 0.0 0.0 0.0 0.0 4 2.95 0.0 0.0 0.0 0.0 5 2.95 0.0 0.0 0.0 0.0 6 2.95 0.0 0.0 0.0 0.0 7 2.95 0.0 0.0 0.0 0.0 8 2.95 0.0 0.0 0.0 0.0 9 2.95 0.0 0.0 0.0 0.0 10-11 2.975 0.0 0.0 0.0 0.0 12-13 3.05 0.0 0.0 0.0 0.0 14-15 3.05 0.0 0.0 0.0 0.0 16-17 3.05 0.0 0.0 0.0 0.0 18-19 3.0625 0.0 0.0 0.0 0.0 20-21 3.075 0.0 0.0 0.0 0.0 22-23 3.075 0.0 0.0 0.0 0.0 24-25 3.075 0.0 0.0 0.0 0.0 26-27 3.1 0.0 0.0 0.0 0.0 28-29 3.1 0.0 0.0 0.0 0.0 30-31 3.125 0.0 0.0 0.0 0.0 32-33 3.15 0.0 0.0 0.0 0.0 34-35 3.2 0.0 0.0 0.0 0.0 36-37 3.2375 0.0 0.0 0.0 0.0 38-39 3.25 0.0 0.0 0.0 0.0 40-41 3.25 0.0 0.0 0.0 0.0 42-43 3.25 0.0 0.0 0.0 0.0 44-45 3.25 0.0 0.0 0.0 0.0 46-47 3.25 0.0 0.0 0.0 0.0 48-49 3.275 0.0 0.0 0.0 0.0 50-51 3.275 0.0 0.0 0.0 0.0 52-53 3.275 0.0 0.0 0.0 0.0 54-55 3.275 0.0 0.0 0.0 0.0 56-57 3.275 0.0 0.0 0.0 0.0 58-59 3.275 0.0 0.0 0.0 0.0 60-61 3.3 0.0 0.0 0.0 0.0 62-63 3.325 0.0 0.0 0.0 0.0 64-65 3.35 0.0 0.0 0.0 0.0 66-67 3.35 0.0 0.0 0.0 0.0 68-69 3.35 0.0 0.0 0.0 0.0 70-71 3.35 0.0 0.0 0.0 0.0 72-73 3.3625 0.0 0.0 0.0 0.0 74-75 3.375 0.0 0.0 0.0 0.0 76-77 3.375 0.0 0.0 0.0 0.0 78-79 3.4 0.0 0.0 0.0 0.0 80-81 3.425 0.0 0.0 0.0 0.0 82-83 3.4375 0.0 0.0 0.0 0.0 84-85 3.5 0.0 0.0 0.0 0.0 86-87 3.5 0.0 0.0 0.0 0.0 88 3.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 3497377 spots for SRR10225135.sra Written 3497377 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra Read 3497361 spots for SRR10225135.sra Written 3497361 spots for SRR10225135.sra SRR ids: ['SRR10225135.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hi0pjys5 SRR10225135.sra spots: 69947236 blocks: [[1, 3497361], [3497362, 6994722], [6994723, 10492083], [10492084, 13989444], [13989445, 17486805], [17486806, 20984166], [20984167, 24481527], [24481528, 27978888], [27978889, 31476249], [31476250, 34973610], [34973611, 38470971], [38470972, 41968332], [41968333, 45465693], [45465694, 48963054], [48963055, 52460415], [52460416, 55957776], [55957777, 59455137], [59455138, 62952498], [62952499, 66449859], [66449860, 69947236]] SRR10225135 file size 19125639 SRR10225135 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 SRR10225135 SRR10225135_1.fastq SRR10225135_2.fastq Input file: SRR10225135_1.fastq Paired file: SRR10225135_2.fastq trimmed: SRR10225135-trimmed-pair1.fastq, SRR10225135-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Tue Feb 11 22:17:13 2025 >> started Tue Feb 11 22:19:10 2025 >> done (117.600s) 69947236 read pairs processed; of these: 468155 ( 0.67%) short read pairs filtered out after trimming by size control 2954343 ( 4.22%) empty read pairs filtered out after trimming by size control 66524738 (95.11%) read pairs available; of these: 9401339 (14.13%) trimmed read pairs available after processing 57123399 (85.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 25093 0.04% 19 16081 0.02% 20 20247 0.03% 21 9194 0.01% 22 5539 0.01% 23 6925 0.01% 24 15972 0.02% 25 17055 0.03% 26 12959 0.02% 27 9102 0.01% 28 6187 0.01% 29 7725 0.01% 30 7870 0.01% 31 5454 0.01% 32 5781 0.01% 33 4170 0.01% 34 3410 0.01% 35 3806 0.01% 36 3985 0.01% 37 4436 0.01% 38 4703 0.01% 39 5082 0.01% 40 5842 0.01% 41 6040 0.01% 42 6469 0.01% 43 7335 0.01% 44 7688 0.01% 45 8331 0.01% 46 8685 0.01% 47 9209 0.01% 48 10038 0.02% 49 10716 0.02% 50 11622 0.02% 51 12433 0.02% 52 13359 0.02% 53 14400 0.02% 54 15648 0.02% 55 17902 0.03% 56 18008 0.03% 57 19366 0.03% 58 20706 0.03% 59 114826 0.17% 60 117214 0.18% 61 71429 0.11% 62 76789 0.12% 63 82448 0.12% 64 83128 0.12% 65 87643 0.13% 66 91030 0.14% 67 97973 0.15% 68 97065 0.15% 69 99217 0.15% 70 101782 0.15% 71 99424 0.15% 72 102567 0.15% 73 110605 0.17% 74 111121 0.17% 75 117948 0.18% 76 126638 0.19% 77 116478 0.18% 78 118064 0.18% 79 121862 0.18% 80 124211 0.19% 81 137356 0.21% 82 142721 0.21% 83 151282 0.23% 84 162985 0.24% 85 163235 0.25% 86 152324 0.23% 87 171625 0.26% 88 177905 0.27% 89 194006 0.29% 90 230719 0.35% 91 336383 0.51% 92 238032 0.36% 93 278474 0.42% 94 286202 0.43% 95 1181197 1.78% 96 368368 0.55% 97 482424 0.73% 98 681412 1.02% 99 1170654 1.76% 100 57123399 85.87% 66524738 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=31 prefix-density=0.00 prefix-fanout=1.0 sequence=CAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTCTATAGCCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=225.17 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=18.3 sequence=GAAGAAAATGGCCAAGAGTCAGGATTACTTCTTTAAGGAGTTTTCTAGGGCTATCACCATTCTTTCTGAGAACAACCCACTCACCGGTACCAAGGGTGAGATCAGAAAGCAGTGCACTGTTGCAAACAAGCACCACTAGAAACTTTGATTTGCTACATGTCAAACTCAAGTACTTCTCTTCCTTGTTTACAACGAGGGAGAAGAGTCTGAGATTTGCAGAATAAGATATTTTCTTTAGAAATGGGTGTTGTTATTGCTAGTCAGTGGCAATTAAGATAGTTGTGGTATTAATGTTGGTTTAACTGCCCTGTTTTTAGCCTGGTTAGGCCCGCTCCTCTTGTTGTTGTAACTTGTGGTTTGTGAGATTAATGTTGG criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=3.08 fanout-score-rank=22 prefix-density=0.33 prefix-fanout=2.5 sequence=TTGGTGGCTTGTAGACTGGTGGCTTCTCAAT criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=891.90 fanout-score-rank=1 prefix-density=0.46 prefix-fanout=30.5 sequence=AAAACAAAAATCAGAGTCAATTGTTTATTTTAAATTCCAAACTTCGCACATCATCTAAAGCCTTGTACTCGTAAACCACAAAATCGAAAAAAAAGCGCCTCAATTCATCATCTCCATGCTTCAGCTTCAAGCTT SRR10225135 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 22:19:49 Started mapping on | Feb 11 22:19:49 Finished on | Feb 11 22:26:31 Mapping speed, Million of reads per hour | 595.74 Number of input reads | 66524738 Average input read length | 195 UNIQUE READS: Uniquely mapped reads number | 58425565 Uniquely mapped reads % | 87.83% Average mapped length | 194.92 Number of splices: Total | 25008106 Number of splices: Annotated (sjdb) | 24253821 Number of splices: GT/AG | 24472272 Number of splices: GC/AG | 329802 Number of splices: AT/AC | 35642 Number of splices: Non-canonical | 170390 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 2.53 Insertion rate per base | 0.03% Insertion average length | 2.29 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2773254 % of reads mapped to multiple loci | 4.17% Number of reads mapped to too many loci | 2497040 % of reads mapped to too many loci | 3.75% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.96% % of reads unmapped: other | 0.29% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5648783 5648783 5648783 N_multimapping 2773254 2773254 2773254 N_noFeature 2335551 2809499 57461173 N_ambiguous 937803 439920 10726 UnstrandedReadsAssigned:55152211 PositiveStrandReadsAssigned:55176146 NegativeStrandReadsAssigned:953666 Dataset is classified positive stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR10225135 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR10225135-trimmed-pair1.fastq SRR10225135-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 66,524,738 reads, 57,655,348 reads pseudoaligned [quant] estimated average fragment length: 252.752 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,454 rounds 52401 SRR10225135.ke.tsv 34699 SRR10225135.se.tsv 87100 total ==> SRR10225135.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1766.25 8101.39 56.3493 Potri.005G024800.1.v4.1 1035 783.248 2272 35.636 Potri.004G059700.1.v4.1 961 709.253 814 14.0995 Potri.007G009000.2.v4.1 1416 1164.25 0 0 Potri.003G141000.2.v4.1 2943 2691.25 1758 8.02501 Potri.016G087400.1.v4.1 270 63.7328 4586.27 884.051 Potri.015G069301.1.v4.1 564 312.654 0 0 Potri.010G195200.1.v4.1 1773 1521.25 856.749 6.91886 Potri.012G127500.1.v4.1 977 725.248 21893 370.851 ==> SRR10225135.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 85 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 1599 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 6 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 568 SRR10225135 completed mapping pipeline successfully