Starting /dee2/code/volunteer_pipeline.sh SRR10225141 current disk space = 3052340080640 free memory = 1507260224 SRR10225141 SRAfilesize 9206494141220b40515211c9931e40dd SRR10225141.sra SRR10225141.sra file validated SRR10225141 is paired end SRR10225141 is conventional basespace SRR10225141 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225141_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.89525 34.0 33.0 34.0 31.0 34.0 2 33.09725 34.0 33.0 34.0 31.0 34.0 3 33.18225 34.0 33.0 34.0 31.0 34.0 4 36.499 37.0 37.0 37.0 35.0 37.0 5 36.422 37.0 37.0 37.0 35.0 37.0 6 36.41425 37.0 37.0 37.0 35.0 37.0 7 36.4775 37.0 37.0 37.0 35.0 37.0 8 36.45075 37.0 37.0 37.0 35.0 37.0 9 38.311 39.0 39.0 39.0 37.0 39.0 10-11 38.274625 39.0 39.0 39.0 37.0 39.0 12-13 38.304500000000004 39.0 39.0 39.0 37.0 39.0 14-15 39.894 41.0 40.0 41.0 38.0 41.0 16-17 39.745125 41.0 40.0 41.0 37.5 41.0 18-19 39.805125000000004 41.0 40.0 41.0 38.0 41.0 20-21 39.771375 41.0 40.0 41.0 37.5 41.0 22-23 39.701125 41.0 40.0 41.0 37.0 41.0 24-25 39.669250000000005 41.0 40.0 41.0 37.0 41.0 26-27 39.52825 41.0 40.0 41.0 37.0 41.0 28-29 39.411125 41.0 39.5 41.0 37.0 41.0 30-31 39.2935 41.0 39.0 41.0 36.5 41.0 32-33 39.0905 41.0 39.0 41.0 36.0 41.0 34-35 38.9865 40.0 39.0 41.0 35.0 41.0 36-37 38.788875000000004 40.0 38.0 41.0 35.0 41.0 38-39 38.696124999999995 40.0 38.0 41.0 35.0 41.0 40-41 38.503125 40.0 38.0 41.0 34.5 41.0 42-43 38.272125 40.0 38.0 41.0 34.0 41.0 44-45 38.62775 40.0 38.0 41.0 35.0 41.0 46-47 38.564 40.0 38.0 41.0 35.0 41.0 48-49 38.460375 40.0 38.0 41.0 34.5 41.0 50-51 38.31225 40.0 37.0 41.0 34.0 41.0 52-53 38.085875 40.0 37.0 41.0 34.0 41.0 54-55 37.806125 40.0 36.0 41.0 33.0 41.0 56-57 37.646375 39.5 35.5 41.0 33.0 41.0 58-59 37.239875 39.0 35.0 41.0 33.0 41.0 60-61 36.93575 39.0 35.0 41.0 32.5 41.0 62-63 36.707875 38.0 35.0 41.0 32.5 41.0 64-65 36.352374999999995 37.0 35.0 40.0 32.0 41.0 66-67 36.063625 37.0 35.0 39.5 32.0 41.0 68-69 35.719750000000005 36.0 35.0 39.0 32.0 41.0 70-71 35.502624999999995 36.0 35.0 39.0 32.0 41.0 72-73 35.181625 35.0 35.0 37.5 32.0 40.0 74-75 34.43925 35.0 35.0 37.0 31.0 39.0 76-77 34.146249999999995 35.0 35.0 36.5 31.0 39.0 78-79 33.9 35.0 34.5 36.0 30.5 38.0 80-81 33.626125 35.0 34.0 36.0 30.5 37.0 82-83 33.432874999999996 35.0 34.0 35.0 30.0 37.0 84-85 33.325874999999996 35.0 34.0 35.0 30.0 36.0 86-87 33.087374999999994 35.0 34.0 35.0 29.5 36.0 88-89 32.907 35.0 34.0 35.0 29.0 36.0 90-91 32.77175 35.0 34.0 35.0 29.5 36.0 92-93 32.687124999999995 35.0 34.0 35.0 29.0 35.5 94-95 32.44525 35.0 34.0 35.0 29.0 35.0 96-97 32.2735 35.0 34.0 35.0 28.0 35.0 98-99 32.26375 35.0 34.0 35.0 29.0 35.0 100 32.2125 35.0 34.0 35.0 29.0 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 8 3.0 9 2.0 10 6.0 11 3.0 12 4.0 13 3.0 14 1.0 15 4.0 16 1.0 17 5.0 18 4.0 19 5.0 20 2.0 21 7.0 22 5.0 23 10.0 24 13.0 25 17.0 26 21.0 27 17.0 28 43.0 29 47.0 30 31.0 31 68.0 32 71.0 33 88.0 34 152.0 35 237.0 36 438.0 37 993.0 38 1393.0 39 305.0 40 1.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.104575163398692 35.319255907491204 22.599296128707895 13.976872800402212 2 33.125 32.225 19.2 15.45 3 31.924999999999997 31.65 19.975 16.45 4 28.575 29.575000000000003 22.425 19.425 5 27.500000000000004 31.0 23.775 17.724999999999998 6 32.175 25.775 22.675 19.375 7 30.725 27.625 23.125 18.525 8 25.174999999999997 30.475 26.924999999999997 17.424999999999997 9 26.075 28.599999999999998 24.95 20.375 10-11 26.387500000000003 30.099999999999998 25.0 18.512500000000003 12-13 24.2375 29.7375 26.55 19.475 14-15 24.5125 28.0625 26.875 20.549999999999997 16-17 24.8625 29.2 25.6125 20.325 18-19 24.3875 27.187499999999996 26.650000000000002 21.775 20-21 26.2125 28.512500000000003 25.275 20.0 22-23 24.95 30.2 25.162499999999998 19.6875 24-25 23.175 28.237499999999997 25.9875 22.6 26-27 23.925 28.5625 26.55 20.962500000000002 28-29 23.4375 29.812499999999996 25.8125 20.9375 30-31 24.7375 27.5875 27.6125 20.0625 32-33 25.162499999999998 28.462500000000002 27.1125 19.2625 34-35 24.025 26.875 27.1625 21.9375 36-37 25.0625 28.9 25.9875 20.05 38-39 26.525 28.487499999999997 25.0 19.9875 40-41 23.549999999999997 28.487499999999997 28.287499999999998 19.675 42-43 25.7625 28.849999999999998 26.137500000000003 19.25 44-45 24.224999999999998 28.0625 27.075 20.6375 46-47 25.025 29.1125 27.287499999999998 18.575 48-49 23.9 28.1375 27.425 20.5375 50-51 24.575 28.95 24.6625 21.8125 52-53 26.275 26.724999999999998 26.0125 20.9875 54-55 25.45 27.8625 25.6125 21.075 56-57 24.712500000000002 26.924999999999997 28.4125 19.950000000000003 58-59 24.3875 26.9625 28.3625 20.2875 60-61 23.9875 27.425 26.937499999999996 21.65 62-63 23.75 28.599999999999998 28.15 19.5 64-65 26.8 29.462500000000002 25.2125 18.525 66-67 24.1625 28.525 28.525 18.787499999999998 68-69 23.724999999999998 29.562500000000004 26.4625 20.25 70-71 23.7125 29.862499999999997 26.7625 19.662499999999998 72-73 26.1625 29.15 25.75 18.9375 74-75 25.8 26.6625 28.375 19.162499999999998 76-77 26.424999999999997 27.287499999999998 25.587500000000002 20.7 78-79 26.525 26.224999999999998 26.637499999999996 20.6125 80-81 25.4875 25.724999999999998 27.3375 21.45 82-83 26.05 26.887499999999996 25.912499999999998 21.15 84-85 25.5625 27.175 26.875 20.3875 86-87 25.85 27.487499999999997 26.5375 20.125 88-89 24.65 26.237500000000004 26.0375 23.075000000000003 90-91 27.1375 26.4125 25.424999999999997 21.025 92-93 24.9125 27.6625 26.525 20.9 94-95 24.349999999999998 28.1 28.349999999999998 19.2 96-97 26.424999999999997 27.3875 26.5375 19.650000000000002 98-99 24.0625 27.025 28.3625 20.549999999999997 100 26.05 26.400000000000002 25.75 21.8 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 1.0 8 1.5 9 1.5 10 0.5 11 0.0 12 1.5 13 1.5 14 1.5 15 4.5 16 4.0 17 2.5 18 3.0 19 3.5 20 4.5 21 4.5 22 7.5 23 9.0 24 9.5 25 12.0 26 8.0 27 6.0 28 8.0 29 10.0 30 17.0 31 20.5 32 23.5 33 26.5 34 38.5 35 55.5 36 69.5 37 83.5 38 116.0 39 149.0 40 179.5 41 199.0 42 224.0 43 226.5 44 214.5 45 229.5 46 225.0 47 214.5 48 226.0 49 213.5 50 145.5 51 123.0 52 114.5 53 103.5 54 117.5 55 101.0 56 67.5 57 52.0 58 42.0 59 36.0 60 41.0 61 35.5 62 24.5 63 19.5 64 17.0 65 12.5 66 7.5 67 9.0 68 11.0 69 11.5 70 11.5 71 11.0 72 9.5 73 5.5 74 2.0 75 1.5 76 2.5 77 3.0 78 2.0 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 0.5499999999999999 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 89.125 #Duplication Level Percentage of deduplicated Percentage of total 1 95.56802244039271 85.175 2 3.0855539971949506 5.5 3 0.785413744740533 2.1 4 0.16830294530154277 0.6 5 0.08415147265077139 0.375 6 0.0 0.0 7 0.08415147265077139 0.525 8 0.028050490883590466 0.2 9 0.028050490883590466 0.22499999999999998 >10 0.1402524544179523 3.4750000000000005 >50 0.028050490883590466 1.825 >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 CAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTG 73 1.825 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 48 1.2 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATG 43 1.075 TruSeq Adapter, Index 2 (100% over 49bp) GCGACCCCAGGTCAGGCGGGACTACCCGCTGAGTTTAAGCATATCAATAA 21 0.525 No Hit AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAAC 17 0.42500000000000004 No Hit TTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGACAGTGTCGC 10 0.25 No Hit TTTGACCTCAAATCAGGTAGGAACACCCGCTGAACTTAAGCATATCAATA 9 0.22499999999999998 No Hit AACACGGACCAAGGAGTCTAACATATATGCGAGTGTTAGGGTGATTAAAC 8 0.2 No Hit GGTGTTGCGGGGAATTTGGACTGTTACTTTGAAAAAATTAGAGTGTTTAA 7 0.17500000000000002 No Hit GTGGAGAAAGGTTCCATGTGAACAGTGATTGGACATGGGTTAGTCGATCC 7 0.17500000000000002 No Hit AACCGATTCCCTTGGTGATTCATAATAACTTTTCGAATCGTATGACTTTA 7 0.17500000000000002 No Hit GTCGACGATGAATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGG 5 0.125 No Hit TTGTTGCAGTTAAAAAGCTCGTAGTTGAATTTCGGGGTTAGTAGGTTGGT 5 0.125 No Hit ACGTCGACGATGAATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTA 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 1.375 0.0 0.0 0.0 0.0 2 1.375 0.0 0.0 0.0 0.0 3 1.375 0.0 0.0 0.0 0.0 4 1.375 0.0 0.0 0.0 0.0 5 1.375 0.0 0.0 0.0 0.0 6 1.375 0.0 0.0 0.0 0.0 7 1.375 0.0 0.0 0.0 0.0 8 1.375 0.0 0.0 0.0 0.0 9 1.375 0.0 0.0 0.0 0.0 10-11 1.375 0.0 0.0 0.0 0.0 12-13 1.3875 0.0 0.0 0.0 0.0 14-15 1.4 0.0 0.0 0.0 0.0 16-17 1.4 0.0 0.0 0.0 0.0 18-19 1.4 0.0 0.0 0.0 0.0 20-21 1.4 0.0 0.0 0.0 0.0 22-23 1.4 0.0 0.0 0.0 0.0 24-25 1.4 0.0 0.0 0.0 0.0 26-27 1.4125 0.0 0.0 0.0 0.0 28-29 1.425 0.0 0.0 0.0 0.0 30-31 1.425 0.0 0.0 0.0 0.0 32-33 1.425 0.0 0.0 0.0 0.0 34-35 1.425 0.0 0.0 0.0 0.0 36-37 1.425 0.0 0.0 0.0 0.0 38-39 1.425 0.0 0.0 0.0 0.0 40-41 1.425 0.0 0.0 0.0 0.0 42-43 1.425 0.0 0.0 0.0 0.0 44-45 1.425 0.0 0.0 0.0 0.0 46-47 1.425 0.0 0.0 0.0 0.0 48-49 1.425 0.0 0.0 0.0 0.0 50-51 1.425 0.0 0.0 0.0 0.0 52-53 1.425 0.0 0.0 0.0 0.0 54-55 1.4375 0.0 0.0 0.0 0.0 56-57 1.45 0.0 0.0 0.0 0.0 58-59 1.45 0.0 0.0 0.0 0.0 60-61 1.45 0.0 0.0 0.0 0.0 62-63 1.5 0.0 0.0 0.0 0.0 64-65 1.5 0.0 0.0 0.0 0.0 66-67 1.5 0.0 0.0 0.0 0.0 68-69 1.5 0.0 0.0 0.0 0.0 70-71 1.5 0.0 0.0 0.0 0.0 72-73 1.5 0.0 0.0 0.0 0.0 74-75 1.5 0.0 0.0 0.0 0.0 76-77 1.5 0.0 0.0 0.0 0.0 78-79 1.5125 0.0 0.0 0.0 0.0 80-81 1.525 0.0 0.0 0.0 0.0 82-83 1.525 0.0 0.0 0.0 0.0 84-85 1.575 0.0 0.0 0.0 0.0 86-87 1.6 0.0 0.0 0.0 0.0 88 1.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACGGG 25 4.078156E-7 94.00001 3 CGGGGAA 25 4.078156E-7 94.00001 6 CAACACG 25 4.078156E-7 94.00001 1 ACGGGGA 25 4.078156E-7 94.00001 5 GGGGAAA 25 4.078156E-7 94.00001 7 TTAGTTG 25 4.078156E-7 94.00001 94 CACGGGG 25 4.078156E-7 94.00001 4 GGGAAAC 30 1.2075088E-6 78.333336 8 GGAAACT 30 1.2075088E-6 78.333336 9 AACACGG 30 1.2075088E-6 78.333336 2 ATGGGTG 25 2.748136E-5 47.000004 70-71 AGCTCTT 25 2.748136E-5 47.000004 52-53 GTGCATG 25 2.748136E-5 47.000004 80-81 CTGAGAG 25 2.748136E-5 47.000004 48-49 ACAGACT 25 2.748136E-5 47.000004 42-43 AGGATTG 25 2.748136E-5 47.000004 36-37 TTACCAG 25 2.748136E-5 47.000004 14-15 GACAGAC 25 2.748136E-5 47.000004 42-43 GTTCTTA 25 2.748136E-5 47.000004 90-91 GGCCGTT 25 2.748136E-5 47.000004 86-87 >>END_MODULE SRR10225141 read2 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225141_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.2845 34.0 31.0 34.0 31.0 34.0 2 32.5665 34.0 31.0 34.0 31.0 34.0 3 32.54575 34.0 31.0 34.0 31.0 34.0 4 36.0065 37.0 37.0 37.0 35.0 37.0 5 35.90125 37.0 37.0 37.0 35.0 37.0 6 35.8835 37.0 37.0 37.0 35.0 37.0 7 35.8385 37.0 37.0 37.0 35.0 37.0 8 35.83 37.0 37.0 37.0 35.0 37.0 9 37.681 39.0 39.0 39.0 35.0 39.0 10-11 37.6535 39.0 39.0 39.0 35.0 39.0 12-13 37.634 39.0 39.0 39.0 35.0 39.0 14-15 39.175625 41.0 40.0 41.0 36.5 41.0 16-17 39.16125 41.0 40.0 41.0 36.0 41.0 18-19 39.007625000000004 41.0 40.0 41.0 36.0 41.0 20-21 38.94525 41.0 40.0 41.0 36.0 41.0 22-23 38.875625 41.0 39.5 41.0 36.0 41.0 24-25 38.835750000000004 41.0 39.5 41.0 35.5 41.0 26-27 38.681625 41.0 39.0 41.0 35.0 41.0 28-29 38.578125 41.0 39.0 41.0 35.0 41.0 30-31 38.43725 41.0 39.0 41.0 34.5 41.0 32-33 38.266125 40.0 38.5 41.0 34.0 41.0 34-35 38.104 40.0 38.0 41.0 33.5 41.0 36-37 38.035 40.0 38.0 41.0 34.0 41.0 38-39 37.840374999999995 40.0 38.0 41.0 33.0 41.0 40-41 37.853 40.0 38.0 41.0 33.5 41.0 42-43 37.659375 40.0 38.0 41.0 33.0 41.0 44-45 37.691874999999996 40.0 38.0 41.0 33.0 41.0 46-47 37.96525 40.0 38.0 41.0 34.0 41.0 48-49 37.846125 40.0 38.0 41.0 33.5 41.0 50-51 37.684625 40.0 37.0 41.0 33.0 41.0 52-53 37.47025 40.0 37.0 41.0 33.0 41.0 54-55 37.282375 40.0 36.5 41.0 33.0 41.0 56-57 36.98675 39.5 35.5 41.0 32.5 41.0 58-59 36.757000000000005 39.0 35.5 41.0 32.0 41.0 60-61 36.526624999999996 39.0 35.0 41.0 32.0 41.0 62-63 36.2915 38.5 35.0 41.0 32.0 41.0 64-65 35.695875 37.0 35.0 40.0 31.0 41.0 66-67 35.172875000000005 37.0 35.0 39.5 30.0 41.0 68-69 34.784125 36.0 35.0 39.0 30.0 41.0 70-71 34.443625 36.0 35.0 39.0 30.0 40.5 72-73 33.976 35.0 34.5 37.5 29.0 40.0 74-75 33.68075 35.0 34.0 37.0 29.0 39.0 76-77 33.452 35.0 34.0 37.0 29.0 39.0 78-79 33.182375 35.0 34.0 36.0 29.0 38.0 80-81 32.918125 35.0 34.0 36.0 29.0 37.0 82-83 32.64725 35.0 34.0 35.5 28.5 37.0 84-85 32.487 35.0 34.0 35.0 29.0 36.0 86-87 32.29175 35.0 34.0 35.0 28.5 36.0 88-89 32.117000000000004 35.0 33.5 35.0 28.0 36.0 90-91 31.896625 35.0 33.0 35.0 26.0 36.0 92-93 31.78575 35.0 33.0 35.0 26.0 35.0 94-95 31.646 35.0 33.0 35.0 26.0 35.0 96-97 31.384500000000003 35.0 33.0 35.0 25.0 35.0 98-99 31.273625 35.0 33.0 35.0 24.5 35.0 100 31.21325 35.0 33.0 35.0 25.0 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 27.0 3 12.0 4 3.0 5 7.0 6 4.0 7 9.0 8 4.0 9 3.0 10 4.0 11 6.0 12 7.0 13 6.0 14 4.0 15 11.0 16 3.0 17 3.0 18 6.0 19 6.0 20 11.0 21 7.0 22 10.0 23 13.0 24 21.0 25 28.0 26 42.0 27 21.0 28 22.0 29 33.0 30 40.0 31 65.0 32 67.0 33 87.0 34 137.0 35 186.0 36 440.0 37 1000.0 38 1360.0 39 284.0 40 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.150000000000006 12.525 15.35 31.974999999999998 2 26.150000000000002 5.65 19.375 48.825 3 16.6 6.4 19.075 57.925000000000004 4 18.975 6.175 20.125 54.725 5 20.474999999999998 10.174999999999999 20.8 48.55 6 30.3 11.225 25.924999999999997 32.550000000000004 7 19.075 25.575 32.225 23.125 8 15.725 28.975 34.275 21.025 9 16.425 28.725 31.75 23.1 10-11 17.6625 29.775000000000002 29.95 22.6125 12-13 17.2375 26.2625 30.625000000000004 25.874999999999996 14-15 16.2625 25.674999999999997 32.4 25.662499999999998 16-17 17.549999999999997 26.924999999999997 31.275 24.25 18-19 19.325 27.675 30.25 22.75 20-21 18.8125 28.799999999999997 28.9 23.4875 22-23 19.7 27.900000000000002 29.175 23.225 24-25 19.0125 29.5 28.000000000000004 23.4875 26-27 19.537499999999998 29.1625 29.7 21.6 28-29 20.175 27.975 28.287499999999998 23.5625 30-31 17.9 26.974999999999998 29.15 25.974999999999998 32-33 18.8375 27.55 27.762500000000003 25.85 34-35 18.15 28.0625 27.750000000000004 26.0375 36-37 18.4875 25.7125 29.549999999999997 26.25 38-39 19.4625 27.787499999999998 28.1875 24.5625 40-41 20.45 28.0625 26.75 24.7375 42-43 19.75 29.3875 26.987499999999997 23.875 44-45 19.35 27.650000000000002 28.275 24.725 46-47 18.7625 27.0 27.712500000000002 26.525 48-49 20.962500000000002 27.187499999999996 27.400000000000002 24.45 50-51 19.925 27.900000000000002 26.937499999999996 25.2375 52-53 18.15 29.45 28.625 23.775 54-55 19.375 30.312499999999996 27.05 23.2625 56-57 18.787499999999998 29.349999999999998 28.275 23.5875 58-59 20.0375 26.474999999999998 28.8875 24.6 60-61 18.25 28.8375 26.625 26.2875 62-63 20.1875 28.012500000000003 26.450000000000003 25.35 64-65 19.175 26.05 29.075 25.7 66-67 18.787499999999998 25.5625 29.375 26.275 68-69 17.7 28.0875 29.012500000000003 25.2 70-71 19.6375 27.3125 28.787499999999998 24.2625 72-73 19.925 27.5625 27.5625 24.95 74-75 19.8375 26.637499999999996 28.1625 25.362499999999997 76-77 19.975 27.825 26.237500000000004 25.9625 78-79 20.275000000000002 27.1375 27.500000000000004 25.087500000000002 80-81 20.175 27.650000000000002 26.125 26.05 82-83 18.8125 25.974999999999998 27.500000000000004 27.712500000000002 84-85 18.675 27.3375 27.5875 26.400000000000002 86-87 18.587500000000002 29.1875 26.137500000000003 26.087500000000002 88-89 21.4375 27.0875 25.8 25.674999999999997 90-91 19.662499999999998 28.1 26.987499999999997 25.25 92-93 22.375 25.3 27.3375 24.9875 94-95 21.4375 27.1625 27.3375 24.0625 96-97 20.6375 26.2875 28.262500000000003 24.8125 98-99 20.599999999999998 26.325 28.225 24.85 100 18.625 27.650000000000002 27.325 26.400000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.5 6 1.0 7 0.5 8 0.0 9 0.0 10 0.5 11 1.0 12 1.0 13 0.5 14 0.5 15 1.0 16 1.0 17 3.0 18 3.5 19 3.0 20 5.0 21 5.0 22 6.0 23 6.5 24 7.0 25 10.0 26 11.0 27 18.0 28 19.5 29 17.5 30 20.0 31 26.0 32 42.0 33 46.5 34 58.5 35 73.0 36 82.5 37 113.5 38 129.5 39 151.0 40 184.0 41 170.5 42 151.0 43 173.5 44 195.0 45 205.0 46 210.0 47 209.5 48 192.0 49 151.0 50 137.0 51 135.5 52 110.0 53 94.5 54 90.5 55 70.5 56 66.5 57 90.0 58 95.0 59 89.5 60 79.5 61 53.0 62 35.0 63 24.5 64 16.5 65 15.5 66 13.5 67 10.5 68 12.0 69 9.0 70 6.5 71 7.0 72 7.5 73 9.5 74 7.0 75 2.5 76 1.0 77 0.5 78 0.0 79 0.5 80 0.5 81 0.0 82 0.5 83 0.5 84 0.0 85 0.5 86 0.5 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 83.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 93.02741358760429 78.05 2 3.635280095351609 6.1 3 1.1918951132300357 3.0 4 0.8939213349225268 3.0 5 0.32777115613825986 1.375 6 0.26817640047675806 1.35 7 0.20858164481525626 1.225 8 0.05959475566150178 0.4 9 0.05959475566150178 0.44999999999999996 >10 0.32777115613825986 5.050000000000001 >50 0.0 0.0 >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 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 42 1.05 Illumina Single End PCR Primer 1 (100% over 50bp) GCCCCCAACTATCCCTATTAATCATTACGTCAATCCTAGAAACCAACAAA 34 0.8500000000000001 No Hit CCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGG 25 0.625 No Hit GCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTT 21 0.525 No Hit GCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCC 18 0.44999999999999996 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 11 0.27499999999999997 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 11 0.27499999999999997 No Hit CCCCTCTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCA 10 0.25 No Hit TGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGC 10 0.25 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 10 0.25 No Hit CCCCGTATTGTTATTTATTGTCACTACCTCCCCGTGTCGGGATTGGGTAA 10 0.25 No Hit GCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTC 9 0.22499999999999998 No Hit CCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAA 9 0.22499999999999998 No Hit CCCTTTCAACAATTTCACGTACTGTTTAACTCTCTTTTCAAAGTTCTTTT 8 0.2 No Hit CCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGA 8 0.2 No Hit GCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGC 7 0.17500000000000002 No Hit TCCCCTCTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACC 7 0.17500000000000002 No Hit CCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCT 7 0.17500000000000002 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC 7 0.17500000000000002 No Hit ACCCCGTATTGTTATTTATTGTCACTACCTCCCCGTGTCGGGATTGGGTA 7 0.17500000000000002 No Hit CGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCG 7 0.17500000000000002 No Hit GCTACTATCACCAAGATCTGCACTAGAGGTTGTTCCACTCAAGATCACTC 7 0.17500000000000002 No Hit CCCTCACGGTACTTGTTCGCTATCGGTCTCTCGCCGTTATTTAGCCTTAG 6 0.15 No Hit GCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCG 6 0.15 No Hit GGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTT 6 0.15 No Hit GTTCGCTATCGGTCTCTCGCCGTTATTTAGCCTTAGGAGAAATTTACCTC 6 0.15 No Hit CCCCCAGTCATTTTATGACCACCAAAATTGATGTTAACCAACCACACGGG 6 0.15 No Hit GCCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACA 6 0.15 No Hit AGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGC 6 0.15 No Hit CTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCA 6 0.15 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 6 0.15 No Hit TTCCCTTTCAACAATTTCACGTACTGTTTAACTCTCTTTTCAAAGTTCTT 5 0.125 No Hit CCCCCAACTATCCCTATTAATCATTACGTCAATCCTAGAAACCAACAAAA 5 0.125 No Hit GTCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGG 5 0.125 No Hit CCCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAG 5 0.125 No Hit CGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCAAGATCTGC 5 0.125 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 5 0.125 No Hit GTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCG 5 0.125 No Hit GTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGA 5 0.125 No Hit CGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGC 5 0.125 No Hit CCCCCTCTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACC 5 0.125 No Hit GCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGG 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 1.2 0.0 0.0 0.0 0.0 2 1.2 0.0 0.0 0.0 0.0 3 1.2 0.0 0.0 0.0 0.0 4 1.2 0.0 0.0 0.0 0.0 5 1.2 0.0 0.0 0.0 0.0 6 1.2 0.0 0.0 0.0 0.0 7 1.2 0.0 0.0 0.0 0.0 8 1.2 0.0 0.0 0.0 0.0 9 1.2 0.0 0.0 0.0 0.0 10-11 1.2 0.0 0.0 0.0 0.0 12-13 1.2125 0.0 0.0 0.0 0.0 14-15 1.2375 0.0 0.0 0.0 0.0 16-17 1.25 0.0 0.0 0.0 0.0 18-19 1.25 0.0 0.0 0.0 0.0 20-21 1.25 0.0 0.0 0.0 0.0 22-23 1.25 0.0 0.0 0.0 0.0 24-25 1.275 0.0 0.0 0.0 0.0 26-27 1.2875 0.0 0.0 0.0 0.0 28-29 1.3 0.0 0.0 0.0 0.0 30-31 1.3 0.0 0.0 0.0 0.0 32-33 1.3 0.0 0.0 0.0 0.0 34-35 1.3 0.0 0.0 0.0 0.0 36-37 1.3 0.0 0.0 0.0 0.0 38-39 1.3 0.0 0.0 0.0 0.0 40-41 1.3 0.0 0.0 0.0 0.0 42-43 1.3 0.0 0.0 0.0 0.0 44-45 1.3 0.0 0.0 0.0 0.0 46-47 1.3 0.0 0.0 0.0 0.0 48-49 1.3 0.0 0.0 0.0 0.0 50-51 1.3 0.0 0.0 0.0 0.0 52-53 1.3 0.0 0.0 0.0 0.0 54-55 1.3125 0.0 0.0 0.0 0.0 56-57 1.325 0.0 0.0 0.0 0.0 58-59 1.325 0.0 0.0 0.0 0.0 60-61 1.325 0.0 0.0 0.0 0.0 62-63 1.375 0.0 0.0 0.0 0.0 64-65 1.375 0.0 0.0 0.0 0.0 66-67 1.375 0.0 0.0 0.0 0.0 68-69 1.375 0.0 0.0 0.0 0.0 70-71 1.375 0.0 0.0 0.0 0.0 72-73 1.375 0.0 0.0 0.0 0.0 74-75 1.375 0.0 0.0 0.0 0.0 76-77 1.375 0.0 0.0 0.0 0.0 78-79 1.3875 0.0 0.0 0.0 0.0 80-81 1.4 0.0 0.0 0.0 0.0 82-83 1.4 0.0 0.0 0.0 0.0 84-85 1.45 0.0 0.0 0.0 0.0 86-87 1.475 0.0 0.0 0.0 0.0 88 1.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTACTT 25 0.0048637707 56.4 8 CGGTACT 25 0.0048637707 56.4 7 GTCTCTC 35 0.008330873 26.857141 26-27 >>END_MODULE Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959600 spots for SRR10225141.sra Written 4959600 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra Read 4959594 spots for SRR10225141.sra Written 4959594 spots for SRR10225141.sra SRR ids: ['SRR10225141.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f5feqof2 SRR10225141.sra spots: 99191886 blocks: [[1, 4959594], [4959595, 9919188], [9919189, 14878782], [14878783, 19838376], [19838377, 24797970], [24797971, 29757564], [29757565, 34717158], [34717159, 39676752], [39676753, 44636346], [44636347, 49595940], [49595941, 54555534], [54555535, 59515128], [59515129, 64474722], [64474723, 69434316], [69434317, 74393910], [74393911, 79353504], [79353505, 84313098], [84313099, 89272692], [89272693, 94232286], [94232287, 99191886]] SRR10225141 file size 27126270 SRR10225141 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 SRR10225141 SRR10225141_1.fastq SRR10225141_2.fastq Input file: SRR10225141_1.fastq Paired file: SRR10225141_2.fastq trimmed: SRR10225141-trimmed-pair1.fastq, SRR10225141-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 23:40:42 2025 >> started Tue Feb 11 23:42:21 2025 >> done (99.258s) 99191886 read pairs processed; of these: 513052 ( 0.52%) short read pairs filtered out after trimming by size control 2199792 ( 2.22%) empty read pairs filtered out after trimming by size control 96479042 (97.27%) read pairs available; of these: 12422621 (12.88%) trimmed read pairs available after processing 84056421 (87.12%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12207 0.01% 19 7613 0.01% 20 10267 0.01% 21 4612 0.00% 22 2917 0.00% 23 3575 0.00% 24 7521 0.01% 25 7867 0.01% 26 6450 0.01% 27 4927 0.01% 28 3798 0.00% 29 4542 0.00% 30 4755 0.00% 31 4134 0.00% 32 4460 0.00% 33 4108 0.00% 34 3928 0.00% 35 4408 0.00% 36 4697 0.00% 37 5209 0.01% 38 5723 0.01% 39 6103 0.01% 40 6810 0.01% 41 7329 0.01% 42 7916 0.01% 43 8740 0.01% 44 9374 0.01% 45 9928 0.01% 46 10641 0.01% 47 11312 0.01% 48 12795 0.01% 49 13489 0.01% 50 14508 0.02% 51 15656 0.02% 52 16713 0.02% 53 18250 0.02% 54 19632 0.02% 55 21605 0.02% 56 22601 0.02% 57 24599 0.03% 58 26538 0.03% 59 84778 0.09% 60 92079 0.10% 61 78919 0.08% 62 88471 0.09% 63 95381 0.10% 64 94751 0.10% 65 102500 0.11% 66 112245 0.12% 67 113103 0.12% 68 113793 0.12% 69 119927 0.12% 70 127395 0.13% 71 122098 0.13% 72 126979 0.13% 73 134449 0.14% 74 132370 0.14% 75 138225 0.14% 76 149662 0.16% 77 144437 0.15% 78 144543 0.15% 79 149633 0.16% 80 156705 0.16% 81 165896 0.17% 82 172388 0.18% 83 187351 0.19% 84 196611 0.20% 85 197862 0.21% 86 191685 0.20% 87 219181 0.23% 88 232719 0.24% 89 264781 0.27% 90 306307 0.32% 91 467284 0.48% 92 329043 0.34% 93 422396 0.44% 94 412090 0.43% 95 1644890 1.70% 96 698508 0.72% 97 728647 0.76% 98 981451 1.02% 99 1578831 1.64% 100 84056421 87.12% 96479042 reads passed initial QC criterion=sequence-density sequence-density=1.37 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=18 prefix-density=1.28 prefix-fanout=2.0 sequence=AAGTTGTTGCAGTTAAAAAGCTCGTAGTTG criterion=fanout-score sequence-density=0.34 sequence-density-rank=18 fanout-score=8.78 fanout-score-rank=1 prefix-density=2.91 prefix-fanout=1.0 sequence=GGATTGACAGATTGAGAGCTCTT criterion=sequence-density sequence-density=4.34 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=12 prefix-density=4.60 prefix-fanout=2.0 sequence=GCTATCGGTCTCTCGCC criterion=fanout-score sequence-density=0.24 sequence-density-rank=24 fanout-score=8.50 fanout-score-rank=1 prefix-density=1.99 prefix-fanout=1.0 sequence=ATTTGCTACTATCACCAAGATCT Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found 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 AAGTTGTTGCAGTTAAAAAGCTCGTAGTTG -y GCTATCGGTCTCTCGCC -o SRR10225141 SRR10225141_1.fastq SRR10225141_2.fastq Input file: SRR10225141_1.fastq Paired file: SRR10225141_2.fastq trimmed: SRR10225141-trimmed-pair1.fastq, SRR10225141-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AAGTTGTTGCAGTTAAAAAGCTCGTAGTTG -- paired 3' end adapter sequence (-y): GCTATCGGTCTCTCGCC -- 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 -- number of concurrent threads (-t): 20 Tue Feb 11 23:48:52 2025 >> started Tue Feb 11 23:49:34 2025 >> done (42.061s) 48239521 read pairs processed; of these: 9063 ( 0.02%) short read pairs filtered out after trimming by size control 56386 ( 0.12%) empty read pairs filtered out after trimming by size control 48174072 (99.86%) read pairs available; of these: 3816 ( 0.01%) trimmed read pairs available after processing 48170256 (99.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6021 0.01% 19 3820 0.01% 20 5215 0.01% 21 2361 0.00% 22 1511 0.00% 23 1851 0.00% 24 3738 0.01% 25 3828 0.01% 26 3148 0.01% 27 2428 0.01% 28 1902 0.00% 29 2276 0.00% 30 2402 0.00% 31 2086 0.00% 32 2294 0.00% 33 2095 0.00% 34 1915 0.00% 35 2111 0.00% 36 2348 0.00% 37 2628 0.01% 38 2924 0.01% 39 3053 0.01% 40 3430 0.01% 41 3736 0.01% 42 3995 0.01% 43 4355 0.01% 44 4636 0.01% 45 4966 0.01% 46 5362 0.01% 47 5573 0.01% 48 6468 0.01% 49 6775 0.01% 50 7237 0.02% 51 7818 0.02% 52 8285 0.02% 53 9114 0.02% 54 9784 0.02% 55 10656 0.02% 56 11294 0.02% 57 12404 0.03% 58 13203 0.03% 59 42741 0.09% 60 45654 0.09% 61 39533 0.08% 62 44076 0.09% 63 47552 0.10% 64 47176 0.10% 65 51309 0.11% 66 56047 0.12% 67 56355 0.12% 68 56638 0.12% 69 59549 0.12% 70 63766 0.13% 71 60746 0.13% 72 63768 0.13% 73 67723 0.14% 74 65995 0.14% 75 69056 0.14% 76 74540 0.15% 77 71944 0.15% 78 72099 0.15% 79 74624 0.15% 80 78485 0.16% 81 83375 0.17% 82 86453 0.18% 83 93921 0.19% 84 98563 0.20% 85 99028 0.21% 86 95525 0.20% 87 109914 0.23% 88 116108 0.24% 89 132375 0.27% 90 153358 0.32% 91 233554 0.48% 92 164143 0.34% 93 211397 0.44% 94 205523 0.43% 95 821852 1.71% 96 347843 0.72% 97 364584 0.76% 98 491169 1.02% 99 786865 1.63% 100 41968100 87.12% criterion=sequence-density sequence-density=2.84 sequence-density-rank=1 fanout-score=1.93 fanout-score-rank=19 prefix-density=2.81 prefix-fanout=1.9 sequence=GATTCCCCTAGTAAC criterion=fanout-score sequence-density=0.37 sequence-density-rank=21 fanout-score=2.64 fanout-score-rank=1 prefix-density=0.97 prefix-fanout=1.0 sequence=AATTTTAAATCCATCGGGTTTTA criterion=sequence-density sequence-density=4.14 sequence-density-rank=1 fanout-score=2.18 fanout-score-rank=12 prefix-density=4.42 prefix-fanout=2.0 sequence=GCTATCGGTCTCTCGCC criterion=fanout-score sequence-density=0.24 sequence-density-rank=25 fanout-score=7.89 fanout-score-rank=1 prefix-density=1.84 prefix-fanout=1.0 sequence=ATTTGCTACTATCACCAAGATCT SRR10225141 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 23:50:55 Started mapping on | Feb 11 23:50:56 Finished on | Feb 12 00:24:42 Mapping speed, Million of reads per hour | 171.32 Number of input reads | 96413593 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 47952914 Uniquely mapped reads % | 49.74% Average mapped length | 195.57 Number of splices: Total | 18978009 Number of splices: Annotated (sjdb) | 18449347 Number of splices: GT/AG | 18574738 Number of splices: GC/AG | 262830 Number of splices: AT/AC | 29226 Number of splices: Non-canonical | 111215 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 2.45 Insertion rate per base | 0.03% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3597658 % of reads mapped to multiple loci | 3.73% Number of reads mapped to too many loci | 19098002 % of reads mapped to too many loci | 19.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 22.66% % of reads unmapped: other | 4.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 45024336 45024336 45024336 N_multimapping 3597658 3597658 3597658 N_noFeature 2415194 3081307 46811974 N_ambiguous 816325 332595 11840 UnstrandedReadsAssigned:44721395 PositiveStrandReadsAssigned:44539012 NegativeStrandReadsAssigned:1129100 Dataset is classified positive stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR10225141 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: SRR10225141-trimmed-pair1.fastq SRR10225141-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 96,413,593 reads, 58,893,057 reads pseudoaligned [quant] estimated average fragment length: 257.013 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,180 rounds 52401 SRR10225141.ke.tsv 34699 SRR10225141.se.tsv 87100 total ==> SRR10225141.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1761.99 10637.4 55.8256 Potri.005G024800.1.v4.1 1035 778.987 1021 12.1198 Potri.004G059700.1.v4.1 961 704.997 1845 24.1996 Potri.007G009000.2.v4.1 1416 1159.99 0 0 Potri.003G141000.2.v4.1 2943 2686.99 1813 6.23923 Potri.016G087400.1.v4.1 270 59.3793 3871.58 602.91 Potri.015G069301.1.v4.1 564 308.391 0 0 Potri.010G195200.1.v4.1 1773 1516.99 123.69 0.753968 Potri.012G127500.1.v4.1 977 720.992 5055 64.832 ==> SRR10225141.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 172 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 939 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 8 Potri.001G416900.v4.1 57 Potri.001G452600.v4.1 406 SRR10225141 completed mapping pipeline successfully